Starting phenix.real_space_refine on Sun Feb 25 13:53:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdu_16595/02_2024/8cdu_16595.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdu_16595/02_2024/8cdu_16595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdu_16595/02_2024/8cdu_16595.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdu_16595/02_2024/8cdu_16595.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdu_16595/02_2024/8cdu_16595.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdu_16595/02_2024/8cdu_16595.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1340 5.49 5 S 71 5.16 5 C 27407 2.51 5 N 9534 2.21 5 O 13612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 4": "OE1" <-> "OE2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C GLU 37": "OE1" <-> "OE2" Residue "C GLU 38": "OE1" <-> "OE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C GLU 296": "OE1" <-> "OE2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C GLU 306": "OE1" <-> "OE2" Residue "C GLU 344": "OE1" <-> "OE2" Residue "C GLU 355": "OE1" <-> "OE2" Residue "C GLU 357": "OE1" <-> "OE2" Residue "C GLU 367": "OE1" <-> "OE2" Residue "C GLU 383": "OE1" <-> "OE2" Residue "C GLU 384": "OE1" <-> "OE2" Residue "C GLU 390": "OE1" <-> "OE2" Residue "C GLU 400": "OE1" <-> "OE2" Residue "C GLU 422": "OE1" <-> "OE2" Residue "C GLU 430": "OE1" <-> "OE2" Residue "C GLU 440": "OE1" <-> "OE2" Residue "C GLU 445": "OE1" <-> "OE2" Residue "C GLU 449": "OE1" <-> "OE2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C GLU 457": "OE1" <-> "OE2" Residue "C GLU 461": "OE1" <-> "OE2" Residue "C GLU 476": "OE1" <-> "OE2" Residue "C GLU 477": "OE1" <-> "OE2" Residue "C GLU 481": "OE1" <-> "OE2" Residue "C GLU 488": "OE1" <-> "OE2" Residue "C GLU 521": "OE1" <-> "OE2" Residue "C GLU 522": "OE1" <-> "OE2" Residue "C GLU 551": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 587": "OE1" <-> "OE2" Residue "C GLU 591": "OE1" <-> "OE2" Residue "C GLU 598": "OE1" <-> "OE2" Residue "C GLU 604": "OE1" <-> "OE2" Residue "C GLU 611": "OE1" <-> "OE2" Residue "C GLU 613": "OE1" <-> "OE2" Residue "C GLU 621": "OE1" <-> "OE2" Residue "C GLU 629": "OE1" <-> "OE2" Residue "C GLU 630": "OE1" <-> "OE2" Residue "C GLU 646": "OE1" <-> "OE2" Residue "C GLU 652": "OE1" <-> "OE2" Residue "C GLU 669": "OE1" <-> "OE2" Residue "C GLU 677": "OE1" <-> "OE2" Residue "C GLU 688": "OE1" <-> "OE2" Residue "C GLU 700": "OE1" <-> "OE2" Residue "C GLU 706": "OE1" <-> "OE2" Residue "D GLU 11": "OE1" <-> "OE2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D GLU 118": "OE1" <-> "OE2" Residue "D GLU 122": "OE1" <-> "OE2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D GLU 169": "OE1" <-> "OE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D GLU 223": "OE1" <-> "OE2" Residue "E GLU 19": "OE1" <-> "OE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "E GLU 104": "OE1" <-> "OE2" Residue "E GLU 124": "OE1" <-> "OE2" Residue "E GLU 165": "OE1" <-> "OE2" Residue "E GLU 169": "OE1" <-> "OE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F GLU 25": "OE1" <-> "OE2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F GLU 65": "OE1" <-> "OE2" Residue "F ARG 66": "NH1" <-> "NH2" Residue "F GLU 84": "OE1" <-> "OE2" Residue "F ARG 146": "NH1" <-> "NH2" Residue "F GLU 153": "OE1" <-> "OE2" Residue "F GLU 188": "OE1" <-> "OE2" Residue "F GLU 191": "OE1" <-> "OE2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G GLU 65": "OE1" <-> "OE2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "H GLU 74": "OE1" <-> "OE2" Residue "H ARG 78": "NH1" <-> "NH2" Residue "H ARG 79": "NH1" <-> "NH2" Residue "H GLU 90": "OE1" <-> "OE2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H GLU 118": "OE1" <-> "OE2" Residue "H GLU 123": "OE1" <-> "OE2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "I GLU 23": "OE1" <-> "OE2" Residue "I GLU 38": "OE1" <-> "OE2" Residue "I GLU 43": "OE1" <-> "OE2" Residue "I GLU 50": "OE1" <-> "OE2" Residue "I GLU 71": "OE1" <-> "OE2" Residue "I ARG 96": "NH1" <-> "NH2" Residue "I GLU 126": "OE1" <-> "OE2" Residue "J ARG 27": "NH1" <-> "NH2" Residue "J GLU 37": "OE1" <-> "OE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J GLU 56": "OE1" <-> "OE2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "J ARG 100": "NH1" <-> "NH2" Residue "J GLU 112": "OE1" <-> "OE2" Residue "L GLU 75": "OE1" <-> "OE2" Residue "M ARG 11": "NH1" <-> "NH2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "M GLU 66": "OE1" <-> "OE2" Residue "M GLU 72": "OE1" <-> "OE2" Residue "M ARG 87": "NH1" <-> "NH2" Residue "M ARG 107": "NH1" <-> "NH2" Residue "N GLU 20": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "O GLU 6": "OE1" <-> "OE2" Residue "O GLU 14": "OE1" <-> "OE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 26": "OE1" <-> "OE2" Residue "O ARG 44": "NH1" <-> "NH2" Residue "O ARG 71": "NH1" <-> "NH2" Residue "O GLU 80": "OE1" <-> "OE2" Residue "O ARG 88": "NH1" <-> "NH2" Residue "Q GLU 3": "OE1" <-> "OE2" Residue "R GLU 24": "OE1" <-> "OE2" Residue "R GLU 73": "OE1" <-> "OE2" Residue "S GLU 36": "OE1" <-> "OE2" Residue "S ARG 78": "NH1" <-> "NH2" Residue "T TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 16": "OE1" <-> "OE2" Residue "T GLU 24": "OE1" <-> "OE2" Residue "T GLU 36": "OE1" <-> "OE2" Residue "T GLU 51": "OE1" <-> "OE2" Residue "T ARG 56": "NH1" <-> "NH2" Residue "T GLU 93": "OE1" <-> "OE2" Residue "T GLU 94": "OE1" <-> "OE2" Residue "T GLU 95": "OE1" <-> "OE2" Residue "U GLU 40": "OE1" <-> "OE2" Residue "V GLU 19": "OE1" <-> "OE2" Residue "V GLU 78": "OE1" <-> "OE2" Residue "V GLU 85": "OE1" <-> "OE2" Residue "V GLU 96": "OE1" <-> "OE2" Residue "V GLU 108": "OE1" <-> "OE2" Residue "K GLU 27": "OE1" <-> "OE2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K GLU 66": "OE1" <-> "OE2" Residue "K GLU 99": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 51964 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 28597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1333, 28597 Classifications: {'RNA': 1333} Modifications used: {'rna2p_pur': 113, 'rna2p_pyr': 81, 'rna3p_pur': 643, 'rna3p_pyr': 496} Link IDs: {'rna2p': 194, 'rna3p': 1138} Chain breaks: 3 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 154 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "C" Number of atoms: 5650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 5650 Classifications: {'peptide': 708} Link IDs: {'PTRANS': 27, 'TRANS': 680} Chain: "D" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1757 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "E" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1615 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 3, 'TRANS': 201} Chain: "F" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1490 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 2 Chain: "G" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1170 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 7, 'TRANS': 150} Chain: "H" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1181 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain: "I" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1036 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "J" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 826 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "L" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1052 Classifications: {'peptide': 136} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 128} Chain: "M" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 868 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "N" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 409 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "O" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 710 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "P" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 695 Classifications: {'peptide': 88} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 82} Chain: "Q" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 691 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "R" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 633 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "S" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 637 Classifications: {'peptide': 83} Link IDs: {'TRANS': 82} Chain: "T" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "U" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 518 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "V" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 730 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "K" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 761 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Time building chain proxies: 25.60, per 1000 atoms: 0.49 Number of scatterers: 51964 At special positions: 0 Unit cell: (191.2, 220.8, 205.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 71 16.00 P 1340 15.00 O 13612 8.00 N 9534 7.00 C 27407 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 27 " distance=2.06 Simple disulfide: pdb=" SG CYS N 27 " - pdb=" SG CYS N 43 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 28.79 Conformation dependent library (CDL) restraints added in 4.8 seconds 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5444 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 32 sheets defined 42.2% alpha, 19.0% beta 418 base pairs and 795 stacking pairs defined. Time for finding SS restraints: 25.38 Creating SS restraints... Processing helix chain 'C' and resid 3 through 16 removed outlier: 3.501A pdb=" N GLU C 16 " --> pdb=" O SER C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 31 removed outlier: 3.631A pdb=" N GLU C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU C 29 " --> pdb=" O GLN C 25 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 52 removed outlier: 4.066A pdb=" N VAL C 43 " --> pdb=" O PHE C 39 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LYS C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 45 " --> pdb=" O GLU C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 71 removed outlier: 4.235A pdb=" N LEU C 71 " --> pdb=" O GLU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 209 through 219 Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 241 through 246 Processing helix chain 'C' and resid 289 through 294 removed outlier: 4.229A pdb=" N TYR C 293 " --> pdb=" O ASP C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 308 Processing helix chain 'C' and resid 322 through 327 Processing helix chain 'C' and resid 371 through 379 Processing helix chain 'C' and resid 382 through 389 Processing helix chain 'C' and resid 392 through 414 Processing helix chain 'C' and resid 442 through 467 Processing helix chain 'C' and resid 479 through 490 Processing helix chain 'C' and resid 505 through 516 removed outlier: 3.759A pdb=" N LEU C 509 " --> pdb=" O HIS C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 533 removed outlier: 3.713A pdb=" N ILE C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 576 Processing helix chain 'C' and resid 582 through 623 Proline residue: C 594 - end of helix Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.620A pdb=" N LYS D 28 " --> pdb=" O PRO D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 62 removed outlier: 3.691A pdb=" N THR D 46 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU D 52 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.654A pdb=" N ARG D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS D 115 " --> pdb=" O ILE D 111 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY D 124 " --> pdb=" O MET D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 148 removed outlier: 3.610A pdb=" N VAL D 134 " --> pdb=" O PRO D 130 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL D 135 " --> pdb=" O LYS D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 179 Processing helix chain 'D' and resid 206 through 226 removed outlier: 3.655A pdb=" N MET D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 12 Processing helix chain 'E' and resid 27 through 46 Processing helix chain 'E' and resid 71 through 77 removed outlier: 3.846A pdb=" N GLY E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 95 removed outlier: 3.534A pdb=" N GLY E 95 " --> pdb=" O ASN E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 125 removed outlier: 3.531A pdb=" N GLU E 124 " --> pdb=" O ALA E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 144 removed outlier: 3.744A pdb=" N LYS E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 16 removed outlier: 4.358A pdb=" N LEU F 11 " --> pdb=" O PRO F 7 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER F 12 " --> pdb=" O SER F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 62 Processing helix chain 'F' and resid 64 through 77 removed outlier: 3.774A pdb=" N LYS F 77 " --> pdb=" O ASP F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 93 Processing helix chain 'F' and resid 93 through 101 Processing helix chain 'F' and resid 106 through 116 Processing helix chain 'F' and resid 143 through 146 removed outlier: 3.750A pdb=" N ARG F 146 " --> pdb=" O GLU F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 143 through 146' Processing helix chain 'F' and resid 148 through 154 Processing helix chain 'F' and resid 190 through 200 removed outlier: 3.766A pdb=" N ILE F 194 " --> pdb=" O ASN F 190 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG F 200 " --> pdb=" O GLU F 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 70 Processing helix chain 'G' and resid 109 through 119 Processing helix chain 'G' and resid 132 through 146 Processing helix chain 'G' and resid 149 through 158 Processing helix chain 'H' and resid 20 through 31 Processing helix chain 'H' and resid 35 through 55 removed outlier: 3.595A pdb=" N SER H 39 " --> pdb=" O LYS H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 70 Processing helix chain 'H' and resid 92 through 111 removed outlier: 3.523A pdb=" N THR H 97 " --> pdb=" O PRO H 93 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU H 110 " --> pdb=" O ASN H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 129 Processing helix chain 'H' and resid 133 through 148 Processing helix chain 'I' and resid 5 through 20 Processing helix chain 'I' and resid 30 through 44 Processing helix chain 'I' and resid 97 through 101 Processing helix chain 'I' and resid 114 through 121 Processing helix chain 'J' and resid 34 through 39 Processing helix chain 'J' and resid 41 through 55 Proline residue: J 51 - end of helix Processing helix chain 'J' and resid 71 through 91 removed outlier: 3.941A pdb=" N GLU J 89 " --> pdb=" O ARG J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 101 removed outlier: 3.706A pdb=" N ALA J 101 " --> pdb=" O THR J 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 127 through 131 removed outlier: 3.503A pdb=" N GLY L 131 " --> pdb=" O SER L 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 21 removed outlier: 3.737A pdb=" N TYR M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 49 through 62 removed outlier: 3.807A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 82 removed outlier: 3.506A pdb=" N ASN M 76 " --> pdb=" O GLU M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'N' and resid 40 through 51 Processing helix chain 'O' and resid 5 through 16 Processing helix chain 'O' and resid 24 through 46 removed outlier: 3.715A pdb=" N THR O 45 " --> pdb=" O GLU O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.636A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'P' and resid 52 through 61 Processing helix chain 'P' and resid 67 through 78 Processing helix chain 'P' and resid 78 through 89 removed outlier: 3.550A pdb=" N GLN P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 25 removed outlier: 3.536A pdb=" N LYS R 18 " --> pdb=" O HIS R 14 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR R 25 " --> pdb=" O LYS R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 45 Processing helix chain 'R' and resid 70 through 75 Processing helix chain 'S' and resid 5 through 42 Processing helix chain 'S' and resid 43 through 64 Processing helix chain 'S' and resid 68 through 85 removed outlier: 3.573A pdb=" N LYS S 82 " --> pdb=" O ARG S 78 " (cutoff:3.500A) Processing helix chain 'T' and resid 15 through 33 Processing helix chain 'T' and resid 68 through 82 removed outlier: 3.739A pdb=" N VAL T 72 " --> pdb=" O ASP T 68 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 21 Processing helix chain 'U' and resid 30 through 36 removed outlier: 3.632A pdb=" N LYS U 36 " --> pdb=" O ASP U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 51 Processing helix chain 'U' and resid 53 through 70 Processing helix chain 'V' and resid 56 through 61 removed outlier: 4.149A pdb=" N SER V 60 " --> pdb=" O GLY V 56 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR V 61 " --> pdb=" O SER V 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 56 through 61' Processing helix chain 'V' and resid 61 through 80 removed outlier: 3.773A pdb=" N HIS V 79 " --> pdb=" O GLY V 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 94 through 106 removed outlier: 3.730A pdb=" N GLY V 106 " --> pdb=" O LEU V 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 33 removed outlier: 3.542A pdb=" N LYS K 24 " --> pdb=" O GLN K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 90 removed outlier: 3.538A pdb=" N MET K 88 " --> pdb=" O VAL K 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 22 through 23 Processing sheet with id=AA2, first strand: chain 'C' and resid 75 through 78 Processing sheet with id=AA3, first strand: chain 'C' and resid 194 through 195 removed outlier: 3.846A pdb=" N GLY C 151 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N HIS C 178 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY C 203 " --> pdb=" O LYS C 179 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL C 181 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE C 201 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 249 through 250 removed outlier: 3.580A pdb=" N GLU C 355 " --> pdb=" O THR C 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 258 through 260 removed outlier: 6.139A pdb=" N THR C 258 " --> pdb=" O MET C 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 312 Processing sheet with id=AA7, first strand: chain 'C' and resid 423 through 427 removed outlier: 3.554A pdb=" N VAL C 437 " --> pdb=" O LYS C 424 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 472 through 475 Processing sheet with id=AA9, first strand: chain 'C' and resid 651 through 654 removed outlier: 3.770A pdb=" N ILE C 651 " --> pdb=" O LEU C 647 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU C 646 " --> pdb=" O ILE C 635 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE C 635 " --> pdb=" O GLU C 646 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C 689 " --> pdb=" O GLY C 633 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 666 through 668 Processing sheet with id=AB2, first strand: chain 'D' and resid 16 through 19 removed outlier: 5.558A pdb=" N PHE D 16 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE D 41 " --> pdb=" O PHE D 16 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS D 18 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE D 38 " --> pdb=" O GLU D 34 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU D 34 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE D 40 " --> pdb=" O PHE D 32 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 90 through 92 removed outlier: 6.630A pdb=" N ILE D 67 " --> pdb=" O TYR D 90 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL D 92 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE D 69 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU D 68 " --> pdb=" O PHE D 162 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE D 164 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL D 70 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU D 161 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE D 186 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE D 163 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 20 through 21 removed outlier: 7.668A pdb=" N LYS E 21 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE E 56 " --> pdb=" O LYS E 21 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS E 53 " --> pdb=" O HIS E 68 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS E 68 " --> pdb=" O LYS E 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 147 through 152 removed outlier: 3.904A pdb=" N THR E 150 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR E 167 " --> pdb=" O THR E 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 179 through 189 removed outlier: 6.008A pdb=" N ASP E 180 " --> pdb=" O ARG E 203 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 124 through 125 removed outlier: 3.631A pdb=" N SER F 124 " --> pdb=" O VAL F 121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 12 through 25 removed outlier: 5.465A pdb=" N GLU G 13 " --> pdb=" O GLY G 40 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY G 40 " --> pdb=" O GLU G 13 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU G 15 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL G 38 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR G 17 " --> pdb=" O LEU G 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 85 through 89 Processing sheet with id=AC1, first strand: chain 'H' and resid 73 through 78 Processing sheet with id=AC2, first strand: chain 'I' and resid 24 through 28 removed outlier: 6.702A pdb=" N ILE I 59 " --> pdb=" O PHE I 51 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N PHE I 51 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG I 61 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL I 49 " --> pdb=" O ARG I 61 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE I 63 " --> pdb=" O ARG I 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 66 through 67 Processing sheet with id=AC4, first strand: chain 'I' and resid 76 through 79 Processing sheet with id=AC5, first strand: chain 'I' and resid 76 through 79 removed outlier: 5.319A pdb=" N VAL I 127 " --> pdb=" O SER I 107 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER I 107 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA I 129 " --> pdb=" O ILE I 105 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 6 through 12 Processing sheet with id=AC7, first strand: chain 'L' and resid 43 through 53 removed outlier: 6.630A pdb=" N ARG L 67 " --> pdb=" O THR L 48 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL L 50 " --> pdb=" O TYR L 65 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR L 65 " --> pdb=" O VAL L 50 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR L 52 " --> pdb=" O ARG L 63 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ARG L 63 " --> pdb=" O THR L 52 " (cutoff:3.500A) removed outlier: 13.616A pdb=" N GLU L 75 " --> pdb=" O VAL L 106 " (cutoff:3.500A) removed outlier: 9.898A pdb=" N TYR L 108 " --> pdb=" O GLU L 75 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR L 77 " --> pdb=" O TYR L 108 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE L 110 " --> pdb=" O THR L 77 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR L 79 " --> pdb=" O ILE L 110 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ARG L 112 " --> pdb=" O TYR L 79 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS L 109 " --> pdb=" O ARG L 96 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU L 94 " --> pdb=" O VAL L 111 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N GLY L 113 " --> pdb=" O VAL L 92 " (cutoff:3.500A) removed outlier: 11.930A pdb=" N VAL L 92 " --> pdb=" O GLY L 113 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 56 through 58 removed outlier: 7.341A pdb=" N LYS K 59 " --> pdb=" O ALA K 54 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA K 54 " --> pdb=" O LYS K 59 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER K 61 " --> pdb=" O LEU K 52 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU K 52 " --> pdb=" O SER K 61 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU K 63 " --> pdb=" O THR K 50 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR K 50 " --> pdb=" O GLU K 63 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE K 65 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL K 48 " --> pdb=" O PHE K 65 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET K 67 " --> pdb=" O LYS K 46 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LYS K 46 " --> pdb=" O MET K 67 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N THR K 69 " --> pdb=" O THR K 44 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR K 44 " --> pdb=" O THR K 69 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS K 71 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ASP K 75 " --> pdb=" O GLY K 38 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLY K 38 " --> pdb=" O ASP K 75 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL K 77 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N VAL K 36 " --> pdb=" O VAL K 77 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 56 through 58 removed outlier: 3.602A pdb=" N LYS K 11 " --> pdb=" O ASP K 97 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 48 through 51 removed outlier: 3.525A pdb=" N GLU P 35 " --> pdb=" O VAL P 22 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE P 20 " --> pdb=" O VAL P 37 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR P 39 " --> pdb=" O TYR P 18 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR P 18 " --> pdb=" O THR P 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 9 through 14 removed outlier: 16.649A pdb=" N VAL Q 9 " --> pdb=" O TYR Q 30 " (cutoff:3.500A) removed outlier: 13.171A pdb=" N TYR Q 30 " --> pdb=" O VAL Q 9 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N GLN Q 11 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLU Q 28 " --> pdb=" O GLN Q 11 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N PHE Q 75 " --> pdb=" O LYS Q 45 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS Q 47 " --> pdb=" O PHE Q 75 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU Q 77 " --> pdb=" O LYS Q 47 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N HIS Q 49 " --> pdb=" O LEU Q 77 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLU Q 79 " --> pdb=" O HIS Q 49 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL Q 78 " --> pdb=" O MET Q 64 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N MET Q 64 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL Q 80 " --> pdb=" O LYS Q 62 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS Q 62 " --> pdb=" O VAL Q 80 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 31 through 33 removed outlier: 6.301A pdb=" N VAL R 31 " --> pdb=" O ALA R 50 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N TYR R 52 " --> pdb=" O VAL R 31 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N THR R 33 " --> pdb=" O TYR R 52 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 36 through 47 removed outlier: 7.354A pdb=" N THR T 38 " --> pdb=" O GLN T 66 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N GLN T 66 " --> pdb=" O THR T 38 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N THR T 40 " --> pdb=" O ASN T 64 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASN T 64 " --> pdb=" O THR T 40 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ASP T 42 " --> pdb=" O ILE T 62 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE T 62 " --> pdb=" O ASP T 42 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY T 44 " --> pdb=" O TYR T 60 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR T 60 " --> pdb=" O GLY T 44 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG T 87 " --> pdb=" O ILE T 9 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'V' and resid 43 through 48 removed outlier: 7.058A pdb=" N ILE V 36 " --> pdb=" O ILE V 44 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TRP V 46 " --> pdb=" O VAL V 34 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL V 34 " --> pdb=" O TRP V 46 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER V 48 " --> pdb=" O THR V 32 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR V 32 " --> pdb=" O SER V 48 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLY V 21 " --> pdb=" O GLU V 85 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N THR V 87 " --> pdb=" O GLY V 21 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ALA V 23 " --> pdb=" O THR V 87 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LYS V 89 " --> pdb=" O ALA V 23 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE V 25 " --> pdb=" O LYS V 89 " (cutoff:3.500A) 1078 hydrogen bonds defined for protein. 3099 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1034 hydrogen bonds 1632 hydrogen bond angles 0 basepair planarities 418 basepair parallelities 795 stacking parallelities Total time for adding SS restraints: 39.48 Time building geometry restraints manager: 30.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7707 1.33 - 1.46: 25528 1.46 - 1.60: 19918 1.60 - 1.73: 2457 1.73 - 1.86: 133 Bond restraints: 55743 Sorted by residual: bond pdb=" O3' G A1395 " pdb=" P G A1396 " ideal model delta sigma weight residual 1.607 1.712 -0.105 1.50e-02 4.44e+03 4.88e+01 bond pdb=" O5' A A 364 " pdb=" C5' A A 364 " ideal model delta sigma weight residual 1.420 1.485 -0.065 1.50e-02 4.44e+03 1.90e+01 bond pdb=" O5' U A1088 " pdb=" C5' U A1088 " ideal model delta sigma weight residual 1.420 1.483 -0.063 1.50e-02 4.44e+03 1.79e+01 bond pdb=" P G A 8 " pdb=" O5' G A 8 " ideal model delta sigma weight residual 1.593 1.655 -0.062 1.50e-02 4.44e+03 1.69e+01 bond pdb=" P A B9002 " pdb=" O5' A B9002 " ideal model delta sigma weight residual 1.593 1.655 -0.062 1.50e-02 4.44e+03 1.68e+01 ... (remaining 55738 not shown) Histogram of bond angle deviations from ideal: 95.76 - 103.60: 4534 103.60 - 111.43: 25735 111.43 - 119.27: 27024 119.27 - 127.10: 21307 127.10 - 134.94: 3272 Bond angle restraints: 81872 Sorted by residual: angle pdb=" CA HIS C 656 " pdb=" CB HIS C 656 " pdb=" CG HIS C 656 " ideal model delta sigma weight residual 113.80 123.42 -9.62 1.00e+00 1.00e+00 9.25e+01 angle pdb=" C TYR Q 36 " pdb=" CA TYR Q 36 " pdb=" CB TYR Q 36 " ideal model delta sigma weight residual 110.79 123.57 -12.78 1.68e+00 3.54e-01 5.78e+01 angle pdb=" N ALA G 22 " pdb=" CA ALA G 22 " pdb=" C ALA G 22 " ideal model delta sigma weight residual 107.61 119.29 -11.68 1.74e+00 3.30e-01 4.51e+01 angle pdb=" O3' C A 980 " pdb=" C3' C A 980 " pdb=" C2' C A 980 " ideal model delta sigma weight residual 109.50 119.24 -9.74 1.50e+00 4.44e-01 4.21e+01 angle pdb=" O3' G A 113 " pdb=" C3' G A 113 " pdb=" C2' G A 113 " ideal model delta sigma weight residual 109.50 119.11 -9.61 1.50e+00 4.44e-01 4.11e+01 ... (remaining 81867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 31961 35.76 - 71.52: 3090 71.52 - 107.29: 411 107.29 - 143.05: 29 143.05 - 178.81: 25 Dihedral angle restraints: 35516 sinusoidal: 27085 harmonic: 8431 Sorted by residual: dihedral pdb=" C5' C A 980 " pdb=" C4' C A 980 " pdb=" C3' C A 980 " pdb=" O3' C A 980 " ideal model delta sinusoidal sigma weight residual 147.00 64.69 82.31 1 8.00e+00 1.56e-02 1.30e+02 dihedral pdb=" O4' C A 980 " pdb=" C4' C A 980 " pdb=" C3' C A 980 " pdb=" C2' C A 980 " ideal model delta sinusoidal sigma weight residual 24.00 -44.82 68.82 1 8.00e+00 1.56e-02 9.58e+01 dihedral pdb=" C4' C A 980 " pdb=" C3' C A 980 " pdb=" C2' C A 980 " pdb=" C1' C A 980 " ideal model delta sinusoidal sigma weight residual -35.00 33.06 -68.06 1 8.00e+00 1.56e-02 9.40e+01 ... (remaining 35513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 8062 0.130 - 0.260: 2157 0.260 - 0.390: 50 0.390 - 0.520: 3 0.520 - 0.650: 5 Chirality restraints: 10277 Sorted by residual: chirality pdb=" P G A 8 " pdb=" OP1 G A 8 " pdb=" OP2 G A 8 " pdb=" O5' G A 8 " both_signs ideal model delta sigma weight residual True 2.41 -3.06 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" P A A 979 " pdb=" OP1 A A 979 " pdb=" OP2 A A 979 " pdb=" O5' A A 979 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.36e+00 chirality pdb=" P C A 817 " pdb=" OP1 C A 817 " pdb=" OP2 C A 817 " pdb=" O5' C A 817 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.23e+00 ... (remaining 10274 not shown) Planarity restraints: 5424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 47 " -0.589 9.50e-02 1.11e+02 2.64e-01 4.58e+01 pdb=" NE ARG I 47 " 0.046 2.00e-02 2.50e+03 pdb=" CZ ARG I 47 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG I 47 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG I 47 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 58 " -0.588 9.50e-02 1.11e+02 2.63e-01 4.24e+01 pdb=" NE ARG F 58 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG F 58 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG F 58 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG F 58 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 3 " 0.521 9.50e-02 1.11e+02 2.34e-01 3.77e+01 pdb=" NE ARG F 3 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG F 3 " -0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG F 3 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG F 3 " 0.030 2.00e-02 2.50e+03 ... (remaining 5421 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 7015 2.76 - 3.30: 48667 3.30 - 3.83: 107388 3.83 - 4.37: 133594 4.37 - 4.90: 182786 Nonbonded interactions: 479450 Sorted by model distance: nonbonded pdb=" O2' A A 979 " pdb=" O2 C A 980 " model vdw 2.229 2.440 nonbonded pdb=" O2' U A1072 " pdb=" O5' C A1073 " model vdw 2.242 2.440 nonbonded pdb=" OP2 C A 531 " pdb=" OH TYR L 79 " model vdw 2.242 2.440 nonbonded pdb=" OH TYR N 49 " pdb=" OE2 GLU K 63 " model vdw 2.259 2.440 nonbonded pdb=" O2' A A 190 " pdb=" O5' C A 191 " model vdw 2.296 2.440 ... (remaining 479445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 13.550 Check model and map are aligned: 0.730 Set scattering table: 0.450 Process input model: 168.810 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 190.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.105 55743 Z= 0.579 Angle : 1.552 12.776 81872 Z= 0.989 Chirality : 0.102 0.650 10277 Planarity : 0.020 0.264 5424 Dihedral : 23.320 178.809 30066 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.87 % Allowed : 5.96 % Favored : 93.17 % Rotamer: Outliers : 4.95 % Allowed : 6.74 % Favored : 88.31 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.13), residues: 2884 helix: -2.52 (0.11), residues: 1150 sheet: -2.36 (0.21), residues: 455 loop : -1.82 (0.16), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.008 TRP E 200 HIS 0.016 0.004 HIS L 109 PHE 0.057 0.007 PHE O 15 TYR 0.066 0.008 TYR L 130 ARG 0.037 0.004 ARG F 3 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 656 time to evaluate : 3.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 ARG cc_start: 0.3345 (mtt-85) cc_final: 0.3019 (ptm-80) REVERT: C 67 GLU cc_start: 0.4815 (mm-30) cc_final: 0.4426 (tp30) REVERT: C 68 LYS cc_start: 0.2960 (mmtt) cc_final: 0.2669 (ttpt) REVERT: C 69 MET cc_start: 0.3261 (OUTLIER) cc_final: 0.2398 (tpp) REVERT: C 72 ILE cc_start: 0.3906 (OUTLIER) cc_final: 0.3571 (pt) REVERT: C 101 ASN cc_start: 0.2282 (OUTLIER) cc_final: 0.1826 (t0) REVERT: C 103 LEU cc_start: 0.4234 (OUTLIER) cc_final: 0.3639 (pp) REVERT: C 107 MET cc_start: 0.3554 (mtp) cc_final: 0.3114 (mtt) REVERT: C 195 GLU cc_start: 0.5021 (OUTLIER) cc_final: 0.4018 (tm-30) REVERT: C 199 GLU cc_start: 0.4309 (tt0) cc_final: 0.4083 (tm-30) REVERT: C 218 LYS cc_start: 0.5911 (tttt) cc_final: 0.5361 (mtpp) REVERT: C 230 MET cc_start: 0.3270 (mmm) cc_final: 0.3004 (mtp) REVERT: C 248 ARG cc_start: 0.2078 (mtt-85) cc_final: 0.1655 (mtt-85) REVERT: C 266 ASP cc_start: 0.1718 (OUTLIER) cc_final: 0.0359 (p0) REVERT: C 271 VAL cc_start: 0.5913 (m) cc_final: 0.5687 (p) REVERT: C 281 TYR cc_start: 0.4982 (m-80) cc_final: 0.4711 (m-10) REVERT: C 287 ILE cc_start: 0.2918 (mm) cc_final: 0.2250 (mm) REVERT: C 346 THR cc_start: 0.5897 (m) cc_final: 0.5207 (p) REVERT: C 348 ASN cc_start: 0.2883 (p0) cc_final: 0.2661 (m-40) REVERT: C 360 GLN cc_start: 0.3505 (mt0) cc_final: 0.2678 (mt0) REVERT: C 389 TYR cc_start: 0.5123 (m-80) cc_final: 0.4896 (m-80) REVERT: C 395 MET cc_start: 0.4178 (ttp) cc_final: 0.3886 (ttp) REVERT: C 410 ARG cc_start: 0.4540 (ttp-170) cc_final: 0.4173 (mtm110) REVERT: C 422 GLU cc_start: 0.5569 (mt-10) cc_final: 0.5296 (tm-30) REVERT: C 434 LYS cc_start: 0.4082 (OUTLIER) cc_final: 0.3718 (tptm) REVERT: C 441 ARG cc_start: 0.3849 (mtm180) cc_final: 0.2994 (mtm180) REVERT: C 445 GLU cc_start: 0.6149 (mp0) cc_final: 0.5828 (mp0) REVERT: C 449 GLU cc_start: 0.5223 (tt0) cc_final: 0.4860 (mm-30) REVERT: C 466 MET cc_start: 0.4245 (ttm) cc_final: 0.3355 (mmp) REVERT: C 476 GLU cc_start: 0.5648 (mt-10) cc_final: 0.5145 (tp30) REVERT: C 479 ASN cc_start: 0.5724 (t0) cc_final: 0.5309 (t0) REVERT: C 496 VAL cc_start: 0.6484 (t) cc_final: 0.6215 (p) REVERT: C 518 ASP cc_start: 0.5886 (m-30) cc_final: 0.5652 (t70) REVERT: C 556 PHE cc_start: 0.4347 (t80) cc_final: 0.3938 (t80) REVERT: C 572 ILE cc_start: 0.4075 (mt) cc_final: 0.3454 (mt) REVERT: C 575 TYR cc_start: 0.4851 (m-80) cc_final: 0.4508 (m-80) REVERT: C 578 ASN cc_start: 0.3169 (m-40) cc_final: 0.2955 (m110) REVERT: C 604 GLU cc_start: 0.5670 (tt0) cc_final: 0.5092 (tm-30) REVERT: C 613 GLU cc_start: 0.5969 (tt0) cc_final: 0.5476 (tp30) REVERT: C 629 GLU cc_start: 0.3920 (mt-10) cc_final: 0.3376 (mm-30) REVERT: C 656 HIS cc_start: 0.4112 (OUTLIER) cc_final: 0.3600 (m-70) REVERT: C 660 MET cc_start: 0.2913 (mtp) cc_final: 0.2370 (mmm) REVERT: C 678 ARG cc_start: 0.2454 (ttp80) cc_final: 0.1062 (mtt-85) REVERT: C 707 ILE cc_start: 0.5439 (mt) cc_final: 0.4569 (mm) REVERT: D 21 ARG cc_start: 0.6135 (mtp-110) cc_final: 0.5782 (ttm170) REVERT: D 24 ASN cc_start: 0.7912 (t0) cc_final: 0.7658 (t0) REVERT: D 36 ASN cc_start: 0.5290 (m110) cc_final: 0.5080 (m110) REVERT: D 82 GLU cc_start: 0.5407 (mt-10) cc_final: 0.5184 (mm-30) REVERT: D 105 GLU cc_start: 0.6451 (mt-10) cc_final: 0.5995 (mp0) REVERT: D 108 GLN cc_start: 0.6822 (mt0) cc_final: 0.6531 (mm-40) REVERT: D 129 LEU cc_start: 0.5398 (OUTLIER) cc_final: 0.5078 (pp) REVERT: D 132 LYS cc_start: 0.4745 (OUTLIER) cc_final: 0.3939 (tptt) REVERT: D 140 GLU cc_start: 0.6564 (tt0) cc_final: 0.6072 (tp30) REVERT: D 142 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6633 (mm-30) REVERT: D 170 ARG cc_start: 0.5846 (ptt180) cc_final: 0.5417 (ptm160) REVERT: D 178 LYS cc_start: 0.6643 (OUTLIER) cc_final: 0.6415 (tptm) REVERT: D 197 ASP cc_start: 0.6739 (m-30) cc_final: 0.6321 (t0) REVERT: D 204 ASP cc_start: 0.6038 (OUTLIER) cc_final: 0.5483 (p0) REVERT: D 219 ASP cc_start: 0.5317 (m-30) cc_final: 0.5031 (t70) REVERT: D 223 GLU cc_start: 0.5155 (mt-10) cc_final: 0.4713 (mm-30) REVERT: E 26 LYS cc_start: 0.6264 (mttt) cc_final: 0.5330 (tttt) REVERT: E 65 ILE cc_start: 0.6455 (mm) cc_final: 0.6137 (mt) REVERT: E 98 VAL cc_start: 0.5690 (t) cc_final: 0.5217 (p) REVERT: E 126 ARG cc_start: 0.4599 (mtt-85) cc_final: 0.3968 (tpp-160) REVERT: E 135 GLN cc_start: 0.6075 (tt0) cc_final: 0.5719 (mm-40) REVERT: E 148 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7892 (m) REVERT: E 163 ARG cc_start: 0.3528 (OUTLIER) cc_final: 0.1926 (tmt170) REVERT: E 205 GLU cc_start: 0.6704 (mt-10) cc_final: 0.5788 (mm-30) REVERT: F 66 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.7043 (ttm170) REVERT: F 152 LYS cc_start: 0.6498 (mtpp) cc_final: 0.6272 (mttt) REVERT: F 168 ASP cc_start: 0.4952 (t0) cc_final: 0.4730 (m-30) REVERT: F 178 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.5597 (ptt-90) REVERT: G 8 LYS cc_start: 0.6243 (OUTLIER) cc_final: 0.5696 (tmtt) REVERT: G 30 ARG cc_start: 0.7343 (mmm-85) cc_final: 0.6511 (tmm160) REVERT: G 32 ARG cc_start: 0.7750 (mtt90) cc_final: 0.7537 (mtp180) REVERT: G 55 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6769 (tp30) REVERT: G 66 ASP cc_start: 0.8137 (t70) cc_final: 0.7932 (t0) REVERT: G 73 GLU cc_start: 0.7903 (tt0) cc_final: 0.7473 (mt-10) REVERT: G 155 LYS cc_start: 0.7563 (ttmm) cc_final: 0.7094 (mmtm) REVERT: H 13 LEU cc_start: 0.5031 (OUTLIER) cc_final: 0.4827 (mt) REVERT: H 45 LYS cc_start: 0.5180 (mttt) cc_final: 0.4977 (mttp) REVERT: H 59 MET cc_start: 0.3047 (OUTLIER) cc_final: 0.2400 (tmm) REVERT: H 60 GLU cc_start: 0.4194 (tt0) cc_final: 0.3841 (mm-30) REVERT: H 63 GLU cc_start: 0.3757 (mt-10) cc_final: 0.3113 (pt0) REVERT: H 67 LYS cc_start: 0.5733 (ttmt) cc_final: 0.5529 (mtmt) REVERT: H 94 GLU cc_start: 0.4563 (mt-10) cc_final: 0.4358 (mm-30) REVERT: H 103 TRP cc_start: 0.5409 (m-10) cc_final: 0.5064 (m-10) REVERT: H 118 GLU cc_start: 0.6328 (mt-10) cc_final: 0.6047 (tt0) REVERT: I 34 ARG cc_start: 0.6995 (ttm170) cc_final: 0.6361 (ttt180) REVERT: I 35 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6389 (mt-10) REVERT: I 38 GLU cc_start: 0.7715 (tt0) cc_final: 0.7330 (mm-30) REVERT: I 53 GLU cc_start: 0.6985 (mp0) cc_final: 0.6714 (mm-30) REVERT: I 54 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6450 (p0) REVERT: I 55 SER cc_start: 0.5423 (p) cc_final: 0.4843 (m) REVERT: I 56 LYS cc_start: 0.5789 (mttt) cc_final: 0.5376 (mtmt) REVERT: I 71 GLU cc_start: 0.6703 (tp30) cc_final: 0.6298 (tp30) REVERT: I 93 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6349 (mm-30) REVERT: I 99 ASN cc_start: 0.8176 (t0) cc_final: 0.7737 (t0) REVERT: J 38 HIS cc_start: 0.5672 (t70) cc_final: 0.5372 (t70) REVERT: J 50 GLN cc_start: 0.5700 (tt0) cc_final: 0.5358 (mm-40) REVERT: J 68 HIS cc_start: 0.6005 (m-70) cc_final: 0.5002 (p-80) REVERT: J 100 ARG cc_start: 0.6083 (OUTLIER) cc_final: 0.5531 (mmt90) REVERT: J 106 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7376 (tmt-80) REVERT: J 112 GLU cc_start: 0.5780 (OUTLIER) cc_final: 0.4770 (tt0) REVERT: L 3 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.8213 (p) REVERT: L 17 GLU cc_start: 0.5345 (mp0) cc_final: 0.4988 (pm20) REVERT: L 32 LYS cc_start: 0.7162 (mmmt) cc_final: 0.6939 (mtpp) REVERT: L 34 GLU cc_start: 0.5913 (pt0) cc_final: 0.5710 (tt0) REVERT: L 49 ARG cc_start: 0.5681 (ttp-110) cc_final: 0.5014 (mtm110) REVERT: L 69 ARG cc_start: 0.7881 (ttm-80) cc_final: 0.7121 (ttp80) REVERT: L 121 GLU cc_start: 0.6687 (mp0) cc_final: 0.6396 (pt0) REVERT: M 93 ARG cc_start: 0.4299 (mtt180) cc_final: 0.3608 (mtt180) REVERT: N 15 LYS cc_start: 0.4960 (ttpt) cc_final: 0.4705 (tptt) REVERT: N 23 ARG cc_start: 0.7087 (mtp85) cc_final: 0.6282 (ptp-170) REVERT: N 25 GLU cc_start: 0.7522 (mt-10) cc_final: 0.6920 (mm-30) REVERT: N 35 ARG cc_start: 0.7392 (mtt180) cc_final: 0.6279 (mtp-110) REVERT: N 61 TRP cc_start: 0.5046 (t60) cc_final: 0.4252 (p-90) REVERT: O 41 GLU cc_start: 0.7636 (tp30) cc_final: 0.7293 (tm-30) REVERT: O 74 ASP cc_start: 0.7608 (t70) cc_final: 0.7160 (t0) REVERT: O 77 ARG cc_start: 0.7275 (mtp180) cc_final: 0.7030 (mtm-85) REVERT: P 10 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7888 (mtm) REVERT: P 35 GLU cc_start: 0.8512 (tp30) cc_final: 0.8293 (tt0) REVERT: P 54 GLU cc_start: 0.7729 (pp20) cc_final: 0.7391 (tp30) REVERT: Q 6 GLN cc_start: 0.7640 (mp10) cc_final: 0.7066 (tt0) REVERT: Q 7 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8237 (mmt180) REVERT: Q 28 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7522 (mm-30) REVERT: Q 56 LYS cc_start: 0.7586 (mttt) cc_final: 0.7119 (ptmt) REVERT: Q 59 ASP cc_start: 0.8551 (m-30) cc_final: 0.8234 (m-30) REVERT: Q 64 MET cc_start: 0.8550 (ttm) cc_final: 0.8297 (ttm) REVERT: R 16 MET cc_start: 0.6610 (tpp) cc_final: 0.5656 (ptt) REVERT: R 81 LYS cc_start: 0.4060 (OUTLIER) cc_final: 0.2024 (tptt) REVERT: S 14 ASN cc_start: 0.7598 (t0) cc_final: 0.7042 (m-40) REVERT: S 29 ARG cc_start: 0.7036 (mtt90) cc_final: 0.6658 (mtm180) REVERT: S 57 ARG cc_start: 0.7702 (mmp-170) cc_final: 0.7080 (mpt-90) REVERT: T 1 MET cc_start: 0.5197 (ptt) cc_final: 0.4892 (ptp) REVERT: T 2 ARG cc_start: 0.5209 (OUTLIER) cc_final: 0.4712 (ptp-170) REVERT: T 3 LYS cc_start: 0.7333 (mttt) cc_final: 0.6468 (tptp) REVERT: T 28 ASN cc_start: 0.5896 (t0) cc_final: 0.5666 (t0) REVERT: T 92 LYS cc_start: 0.7251 (mtmt) cc_final: 0.6960 (mtmt) REVERT: T 94 GLU cc_start: 0.2900 (OUTLIER) cc_final: 0.2179 (mp0) REVERT: U 21 ASN cc_start: 0.6617 (m110) cc_final: 0.6301 (m110) REVERT: U 32 ASP cc_start: 0.6555 (m-30) cc_final: 0.6276 (p0) REVERT: U 41 ARG cc_start: 0.6217 (mtp180) cc_final: 0.5524 (mtt-85) REVERT: U 47 ARG cc_start: 0.7330 (mtp85) cc_final: 0.5843 (mtm-85) REVERT: U 48 ARG cc_start: 0.6365 (OUTLIER) cc_final: 0.5783 (mtt180) REVERT: K 20 GLN cc_start: 0.6032 (mt0) cc_final: 0.5456 (tt0) REVERT: K 45 GLU cc_start: 0.6586 (mt-10) cc_final: 0.6339 (mm-30) REVERT: K 46 LYS cc_start: 0.6882 (tttm) cc_final: 0.6637 (tttp) REVERT: K 53 ARG cc_start: 0.5910 (mtm-85) cc_final: 0.5658 (ttm110) REVERT: K 57 LYS cc_start: 0.6767 (OUTLIER) cc_final: 0.6498 (tptt) REVERT: K 69 THR cc_start: 0.7425 (m) cc_final: 0.7156 (p) REVERT: K 96 VAL cc_start: 0.7999 (t) cc_final: 0.7762 (m) REVERT: K 98 ILE cc_start: 0.4902 (OUTLIER) cc_final: 0.4641 (mt) REVERT: K 99 GLU cc_start: 0.4156 (tt0) cc_final: 0.3159 (mm-30) outliers start: 124 outliers final: 28 residues processed: 733 average time/residue: 0.7816 time to fit residues: 903.2228 Evaluate side-chains 487 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 427 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 656 HIS Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 130 PRO Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain P residue 10 MET Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain Q residue 7 ARG Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain T residue 2 ARG Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 87 ARG Chi-restraints excluded: chain T residue 94 GLU Chi-restraints excluded: chain U residue 48 ARG Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 98 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 349 optimal weight: 1.9990 chunk 313 optimal weight: 0.9980 chunk 174 optimal weight: 7.9990 chunk 107 optimal weight: 10.9990 chunk 211 optimal weight: 4.9990 chunk 167 optimal weight: 20.0000 chunk 324 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 197 optimal weight: 7.9990 chunk 241 optimal weight: 2.9990 chunk 375 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 GLN C 671 HIS C 697 ASN D 44 GLN ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN G 70 ASN H 64 GLN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 GLN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN L 18 ASN M 105 ASN O 18 HIS O 37 ASN O 40 ASN O 46 HIS O 72 ASN O 83 ASN P 72 ASN ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN R 57 HIS S 84 ASN T 33 ASN T 61 GLN T 66 GLN ** V 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 30 ASN V 42 ASN K 56 HIS ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 55743 Z= 0.253 Angle : 0.723 8.313 81872 Z= 0.382 Chirality : 0.044 0.359 10277 Planarity : 0.006 0.090 5424 Dihedral : 23.991 177.166 24295 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.71 % Favored : 96.01 % Rotamer: Outliers : 5.15 % Allowed : 11.25 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.14), residues: 2884 helix: 0.05 (0.14), residues: 1160 sheet: -1.43 (0.21), residues: 487 loop : -1.30 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 200 HIS 0.006 0.001 HIS R 14 PHE 0.025 0.002 PHE C 6 TYR 0.026 0.002 TYR L 130 ARG 0.007 0.001 ARG M 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 432 time to evaluate : 3.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 55 ILE cc_start: 0.0365 (pt) cc_final: -0.0046 (mm) REVERT: C 59 ARG cc_start: 0.3345 (mtt-85) cc_final: 0.2974 (ppt170) REVERT: C 68 LYS cc_start: 0.3045 (mmtt) cc_final: 0.2794 (ttpt) REVERT: C 101 ASN cc_start: 0.2072 (OUTLIER) cc_final: 0.1667 (t0) REVERT: C 103 LEU cc_start: 0.4229 (OUTLIER) cc_final: 0.3610 (pp) REVERT: C 137 ILE cc_start: 0.4873 (mt) cc_final: 0.4616 (tt) REVERT: C 218 LYS cc_start: 0.5782 (tttt) cc_final: 0.5135 (tppt) REVERT: C 224 GLU cc_start: 0.4154 (mt-10) cc_final: 0.3842 (mp0) REVERT: C 230 MET cc_start: 0.2905 (mmm) cc_final: 0.2648 (mtp) REVERT: C 266 ASP cc_start: 0.1650 (OUTLIER) cc_final: 0.0233 (p0) REVERT: C 277 ASP cc_start: 0.4841 (m-30) cc_final: 0.4365 (t0) REVERT: C 287 ILE cc_start: 0.2986 (mm) cc_final: 0.2392 (mm) REVERT: C 395 MET cc_start: 0.4114 (ttp) cc_final: 0.3835 (ttp) REVERT: C 434 LYS cc_start: 0.3944 (OUTLIER) cc_final: 0.3698 (tttp) REVERT: C 445 GLU cc_start: 0.6235 (mp0) cc_final: 0.5950 (mp0) REVERT: C 457 GLU cc_start: 0.6059 (mt-10) cc_final: 0.5759 (tm-30) REVERT: C 466 MET cc_start: 0.4236 (ttm) cc_final: 0.3553 (mmp) REVERT: C 485 LYS cc_start: 0.6613 (mttt) cc_final: 0.6098 (ptmm) REVERT: C 531 ARG cc_start: 0.4171 (mtt180) cc_final: 0.3869 (mmm160) REVERT: C 556 PHE cc_start: 0.4105 (t80) cc_final: 0.3689 (t80) REVERT: C 573 ARG cc_start: 0.3417 (ttm-80) cc_final: 0.2503 (mtp-110) REVERT: C 575 TYR cc_start: 0.5036 (m-80) cc_final: 0.4549 (m-10) REVERT: C 604 GLU cc_start: 0.5535 (tt0) cc_final: 0.4945 (tm-30) REVERT: C 629 GLU cc_start: 0.4321 (mt-10) cc_final: 0.3581 (mm-30) REVERT: C 660 MET cc_start: 0.2720 (mtp) cc_final: 0.2342 (mmm) REVERT: C 678 ARG cc_start: 0.2288 (ttp80) cc_final: 0.1024 (mtt90) REVERT: C 707 ILE cc_start: 0.5413 (mt) cc_final: 0.4516 (mm) REVERT: D 21 ARG cc_start: 0.6062 (mtp-110) cc_final: 0.5807 (ttm110) REVERT: D 22 ARG cc_start: 0.6085 (OUTLIER) cc_final: 0.5368 (ttt180) REVERT: D 78 ASP cc_start: 0.6003 (OUTLIER) cc_final: 0.4844 (t70) REVERT: D 105 GLU cc_start: 0.6240 (mt-10) cc_final: 0.5826 (mp0) REVERT: D 108 GLN cc_start: 0.6509 (mt0) cc_final: 0.6183 (mm-40) REVERT: D 132 LYS cc_start: 0.4337 (OUTLIER) cc_final: 0.3701 (tptt) REVERT: D 140 GLU cc_start: 0.6018 (tt0) cc_final: 0.5477 (mm-30) REVERT: D 142 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6503 (mm-30) REVERT: D 170 ARG cc_start: 0.5701 (ptt180) cc_final: 0.5331 (ptm160) REVERT: D 204 ASP cc_start: 0.5965 (OUTLIER) cc_final: 0.5343 (p0) REVERT: D 219 ASP cc_start: 0.5454 (m-30) cc_final: 0.5075 (t70) REVERT: E 26 LYS cc_start: 0.6344 (mttt) cc_final: 0.5608 (tttt) REVERT: E 65 ILE cc_start: 0.6437 (OUTLIER) cc_final: 0.6141 (mt) REVERT: E 98 VAL cc_start: 0.5657 (t) cc_final: 0.5305 (p) REVERT: E 103 LEU cc_start: 0.4717 (mm) cc_final: 0.4266 (mt) REVERT: E 126 ARG cc_start: 0.4703 (mtt-85) cc_final: 0.3951 (tpp-160) REVERT: E 163 ARG cc_start: 0.3656 (OUTLIER) cc_final: 0.2009 (ttt180) REVERT: E 205 GLU cc_start: 0.6514 (mt-10) cc_final: 0.5732 (mm-30) REVERT: F 152 LYS cc_start: 0.6395 (mtpp) cc_final: 0.6139 (mttt) REVERT: F 178 ARG cc_start: 0.5906 (OUTLIER) cc_final: 0.5172 (ptt-90) REVERT: G 8 LYS cc_start: 0.6239 (OUTLIER) cc_final: 0.5686 (tmtt) REVERT: G 30 ARG cc_start: 0.7378 (mmm-85) cc_final: 0.6442 (tmm160) REVERT: G 88 ARG cc_start: 0.7680 (mtt-85) cc_final: 0.7256 (ttt90) REVERT: G 155 LYS cc_start: 0.7432 (ttmm) cc_final: 0.6931 (mmtm) REVERT: H 13 LEU cc_start: 0.4785 (OUTLIER) cc_final: 0.4547 (mt) REVERT: H 30 MET cc_start: 0.6180 (OUTLIER) cc_final: 0.5454 (mpp) REVERT: H 59 MET cc_start: 0.2697 (tpt) cc_final: 0.2448 (tmm) REVERT: H 60 GLU cc_start: 0.4775 (tt0) cc_final: 0.4359 (mt-10) REVERT: H 70 MET cc_start: 0.5357 (mtp) cc_final: 0.5026 (mtm) REVERT: H 86 GLN cc_start: 0.3429 (mm-40) cc_final: 0.3085 (mm-40) REVERT: H 94 GLU cc_start: 0.4414 (mt-10) cc_final: 0.4152 (mm-30) REVERT: H 103 TRP cc_start: 0.5388 (m-10) cc_final: 0.5120 (m-10) REVERT: H 116 MET cc_start: 0.5236 (tpt) cc_final: 0.5002 (tpp) REVERT: I 34 ARG cc_start: 0.7136 (ttm170) cc_final: 0.6491 (ttt180) REVERT: I 35 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6240 (mt-10) REVERT: I 38 GLU cc_start: 0.7682 (tt0) cc_final: 0.7291 (mm-30) REVERT: I 53 GLU cc_start: 0.7024 (mp0) cc_final: 0.6521 (mm-30) REVERT: I 55 SER cc_start: 0.5278 (p) cc_final: 0.5041 (m) REVERT: I 71 GLU cc_start: 0.6869 (tp30) cc_final: 0.6359 (tp30) REVERT: I 93 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6274 (mm-30) REVERT: I 99 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7836 (t0) REVERT: J 12 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.5405 (ttm170) REVERT: J 50 GLN cc_start: 0.5023 (tt0) cc_final: 0.4791 (mm-40) REVERT: J 66 ASN cc_start: 0.5726 (t0) cc_final: 0.5362 (t0) REVERT: J 100 ARG cc_start: 0.6280 (OUTLIER) cc_final: 0.5647 (mmt90) REVERT: J 112 GLU cc_start: 0.5809 (OUTLIER) cc_final: 0.4714 (tt0) REVERT: L 17 GLU cc_start: 0.5146 (mp0) cc_final: 0.4942 (pm20) REVERT: L 32 LYS cc_start: 0.7069 (mmmt) cc_final: 0.6688 (mtmm) REVERT: L 36 THR cc_start: 0.7468 (OUTLIER) cc_final: 0.6988 (p) REVERT: L 49 ARG cc_start: 0.5514 (ttp-110) cc_final: 0.4868 (mtm110) REVERT: L 69 ARG cc_start: 0.7921 (ttm-80) cc_final: 0.7050 (tmt170) REVERT: N 23 ARG cc_start: 0.7343 (mtp85) cc_final: 0.6358 (ptp-170) REVERT: N 25 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6713 (mm-30) REVERT: N 35 ARG cc_start: 0.7149 (mtt180) cc_final: 0.6258 (mtp-110) REVERT: N 50 LYS cc_start: 0.6902 (mtmt) cc_final: 0.6686 (mttt) REVERT: P 35 GLU cc_start: 0.8557 (tp30) cc_final: 0.8292 (tt0) REVERT: Q 6 GLN cc_start: 0.7644 (mp10) cc_final: 0.7416 (mt0) REVERT: Q 59 ASP cc_start: 0.8516 (m-30) cc_final: 0.8314 (m-30) REVERT: Q 82 GLU cc_start: 0.6193 (tt0) cc_final: 0.5857 (mm-30) REVERT: R 16 MET cc_start: 0.6453 (tpp) cc_final: 0.5586 (ptt) REVERT: R 52 TYR cc_start: 0.6411 (t80) cc_final: 0.6134 (t80) REVERT: R 81 LYS cc_start: 0.4098 (OUTLIER) cc_final: 0.1709 (pptt) REVERT: S 29 ARG cc_start: 0.6828 (mtt90) cc_final: 0.6488 (mtm110) REVERT: T 1 MET cc_start: 0.5257 (ptt) cc_final: 0.4543 (ptp) REVERT: T 2 ARG cc_start: 0.4397 (OUTLIER) cc_final: 0.4149 (ptp-170) REVERT: T 3 LYS cc_start: 0.7100 (mttt) cc_final: 0.6375 (tptt) REVERT: T 23 ILE cc_start: 0.4946 (OUTLIER) cc_final: 0.4728 (tp) REVERT: T 66 GLN cc_start: 0.5987 (mt0) cc_final: 0.5508 (tt0) REVERT: U 21 ASN cc_start: 0.6596 (m110) cc_final: 0.6254 (m110) REVERT: U 32 ASP cc_start: 0.6567 (m-30) cc_final: 0.6241 (p0) REVERT: U 33 LEU cc_start: 0.6675 (tp) cc_final: 0.6414 (mt) REVERT: U 41 ARG cc_start: 0.5939 (mtp180) cc_final: 0.5341 (mtt-85) REVERT: U 47 ARG cc_start: 0.7211 (mtp85) cc_final: 0.6128 (mtm-85) REVERT: U 48 ARG cc_start: 0.6289 (OUTLIER) cc_final: 0.5808 (mtt180) REVERT: K 20 GLN cc_start: 0.5929 (mt0) cc_final: 0.5469 (tt0) REVERT: K 40 ILE cc_start: 0.6426 (mp) cc_final: 0.6212 (mm) REVERT: K 45 GLU cc_start: 0.6473 (mt-10) cc_final: 0.6240 (mm-30) REVERT: K 53 ARG cc_start: 0.5980 (mtm-85) cc_final: 0.5600 (ttm110) REVERT: K 69 THR cc_start: 0.7500 (m) cc_final: 0.7163 (p) REVERT: K 96 VAL cc_start: 0.7910 (t) cc_final: 0.7479 (m) outliers start: 129 outliers final: 72 residues processed: 525 average time/residue: 0.7370 time to fit residues: 610.4978 Evaluate side-chains 445 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 350 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain T residue 2 ARG Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 20 SER Chi-restraints excluded: chain U residue 48 ARG Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 208 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 312 optimal weight: 0.9980 chunk 256 optimal weight: 0.0170 chunk 103 optimal weight: 10.0000 chunk 376 optimal weight: 5.9990 chunk 406 optimal weight: 8.9990 chunk 335 optimal weight: 0.0050 chunk 373 optimal weight: 0.9990 chunk 128 optimal weight: 20.0000 chunk 302 optimal weight: 8.9990 overall best weight: 1.6036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 ASN C 360 GLN D 18 HIS E 68 HIS ** E 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 GLN H 129 ASN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 ASN ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 ASN O 38 ASN O 83 ASN ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN S 70 ASN V 40 HIS ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 55743 Z= 0.165 Angle : 0.591 12.001 81872 Z= 0.311 Chirality : 0.038 0.343 10277 Planarity : 0.004 0.066 5424 Dihedral : 23.757 179.712 24246 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.29 % Favored : 96.46 % Rotamer: Outliers : 4.07 % Allowed : 13.84 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 2884 helix: 1.07 (0.15), residues: 1176 sheet: -0.82 (0.22), residues: 515 loop : -0.92 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP V 46 HIS 0.006 0.001 HIS V 40 PHE 0.019 0.002 PHE C 6 TYR 0.021 0.002 TYR K 58 ARG 0.006 0.000 ARG E 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 396 time to evaluate : 3.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 14 MET cc_start: 0.1872 (mtt) cc_final: 0.1606 (mtm) REVERT: C 55 ILE cc_start: 0.0138 (pt) cc_final: -0.0116 (tt) REVERT: C 68 LYS cc_start: 0.3016 (mmtt) cc_final: 0.2724 (ttpt) REVERT: C 101 ASN cc_start: 0.2378 (OUTLIER) cc_final: 0.1819 (t0) REVERT: C 131 ARG cc_start: 0.5111 (ttt180) cc_final: 0.3497 (ptp-110) REVERT: C 133 LEU cc_start: 0.3161 (OUTLIER) cc_final: 0.2914 (mt) REVERT: C 172 ASN cc_start: 0.6105 (OUTLIER) cc_final: 0.5341 (t0) REVERT: C 218 LYS cc_start: 0.5875 (tttt) cc_final: 0.5249 (tppt) REVERT: C 230 MET cc_start: 0.2902 (mmm) cc_final: 0.2619 (mtp) REVERT: C 266 ASP cc_start: 0.1739 (OUTLIER) cc_final: -0.0456 (p0) REVERT: C 277 ASP cc_start: 0.4717 (m-30) cc_final: 0.4249 (t0) REVERT: C 346 THR cc_start: 0.5395 (OUTLIER) cc_final: 0.4964 (p) REVERT: C 399 MET cc_start: 0.3611 (ptt) cc_final: 0.3334 (ptp) REVERT: C 445 GLU cc_start: 0.6319 (mp0) cc_final: 0.6083 (mp0) REVERT: C 457 GLU cc_start: 0.5934 (mt-10) cc_final: 0.5678 (tm-30) REVERT: C 466 MET cc_start: 0.4053 (ttm) cc_final: 0.3302 (mmp) REVERT: C 504 ILE cc_start: 0.5963 (OUTLIER) cc_final: 0.5728 (pt) REVERT: C 531 ARG cc_start: 0.4269 (mtt180) cc_final: 0.3889 (mmt180) REVERT: C 556 PHE cc_start: 0.4065 (t80) cc_final: 0.3639 (t80) REVERT: C 575 TYR cc_start: 0.5078 (m-80) cc_final: 0.4546 (m-10) REVERT: C 604 GLU cc_start: 0.5723 (tt0) cc_final: 0.5133 (tm-30) REVERT: C 629 GLU cc_start: 0.3784 (mt-10) cc_final: 0.3406 (mm-30) REVERT: C 678 ARG cc_start: 0.2190 (ttp80) cc_final: 0.0999 (mtt180) REVERT: C 710 MET cc_start: 0.4500 (tmm) cc_final: 0.2972 (mpp) REVERT: D 21 ARG cc_start: 0.6008 (mtp-110) cc_final: 0.5707 (ttm110) REVERT: D 22 ARG cc_start: 0.6081 (OUTLIER) cc_final: 0.5367 (ttt180) REVERT: D 105 GLU cc_start: 0.6225 (mt-10) cc_final: 0.5871 (mp0) REVERT: D 108 GLN cc_start: 0.6570 (mt0) cc_final: 0.6194 (mm-40) REVERT: D 142 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6521 (mm-30) REVERT: D 170 ARG cc_start: 0.5704 (ptt180) cc_final: 0.5324 (ptm160) REVERT: D 204 ASP cc_start: 0.5705 (OUTLIER) cc_final: 0.5113 (p0) REVERT: D 219 ASP cc_start: 0.5617 (m-30) cc_final: 0.5140 (t70) REVERT: D 223 GLU cc_start: 0.5053 (mt-10) cc_final: 0.4748 (mm-30) REVERT: E 26 LYS cc_start: 0.6059 (mttt) cc_final: 0.5456 (tttt) REVERT: E 65 ILE cc_start: 0.6321 (OUTLIER) cc_final: 0.5867 (mt) REVERT: E 103 LEU cc_start: 0.4780 (mm) cc_final: 0.4323 (mt) REVERT: E 126 ARG cc_start: 0.4702 (mtt-85) cc_final: 0.3936 (tpp-160) REVERT: E 138 GLN cc_start: 0.5885 (mt0) cc_final: 0.5655 (mp10) REVERT: E 141 MET cc_start: 0.6059 (mmm) cc_final: 0.5571 (mmm) REVERT: E 163 ARG cc_start: 0.3586 (OUTLIER) cc_final: 0.1947 (ttt180) REVERT: E 187 GLU cc_start: 0.5224 (mt-10) cc_final: 0.4853 (pt0) REVERT: F 152 LYS cc_start: 0.6389 (mtpp) cc_final: 0.6137 (mttt) REVERT: F 178 ARG cc_start: 0.5713 (OUTLIER) cc_final: 0.5019 (ptt-90) REVERT: G 8 LYS cc_start: 0.6272 (OUTLIER) cc_final: 0.5807 (tmtt) REVERT: G 30 ARG cc_start: 0.7251 (mmm-85) cc_final: 0.6558 (ttp-170) REVERT: G 88 ARG cc_start: 0.7645 (mtt-85) cc_final: 0.6847 (ttp-170) REVERT: G 155 LYS cc_start: 0.7443 (ttmm) cc_final: 0.6944 (mmtm) REVERT: H 30 MET cc_start: 0.6058 (mtm) cc_final: 0.5454 (mpp) REVERT: H 60 GLU cc_start: 0.5195 (tt0) cc_final: 0.4728 (mt-10) REVERT: H 70 MET cc_start: 0.5171 (mtt) cc_final: 0.4856 (mtm) REVERT: H 86 GLN cc_start: 0.3501 (OUTLIER) cc_final: 0.3174 (mm-40) REVERT: H 94 GLU cc_start: 0.4046 (mt-10) cc_final: 0.3712 (mm-30) REVERT: H 139 GLU cc_start: 0.5054 (tt0) cc_final: 0.4576 (tp30) REVERT: I 34 ARG cc_start: 0.7151 (ttm170) cc_final: 0.6500 (ttt180) REVERT: I 38 GLU cc_start: 0.7715 (tt0) cc_final: 0.7440 (mm-30) REVERT: I 47 ARG cc_start: 0.7671 (mtt90) cc_final: 0.6679 (ttp-110) REVERT: I 53 GLU cc_start: 0.6910 (mp0) cc_final: 0.6472 (mm-30) REVERT: I 55 SER cc_start: 0.5532 (p) cc_final: 0.5283 (m) REVERT: I 71 GLU cc_start: 0.6853 (tp30) cc_final: 0.6517 (tp30) REVERT: I 93 GLU cc_start: 0.6621 (mt-10) cc_final: 0.6416 (mm-30) REVERT: I 99 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7697 (t0) REVERT: J 12 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.5502 (ttm110) REVERT: J 66 ASN cc_start: 0.5618 (t0) cc_final: 0.5167 (t0) REVERT: J 68 HIS cc_start: 0.5506 (m-70) cc_final: 0.4454 (p-80) REVERT: J 81 HIS cc_start: 0.7133 (t70) cc_final: 0.6890 (t70) REVERT: J 100 ARG cc_start: 0.6320 (OUTLIER) cc_final: 0.5597 (mmt90) REVERT: J 112 GLU cc_start: 0.5695 (OUTLIER) cc_final: 0.4747 (tt0) REVERT: L 17 GLU cc_start: 0.5201 (mp0) cc_final: 0.4886 (pm20) REVERT: L 32 LYS cc_start: 0.7038 (mmmt) cc_final: 0.6804 (mtpt) REVERT: L 36 THR cc_start: 0.7579 (OUTLIER) cc_final: 0.7141 (p) REVERT: L 49 ARG cc_start: 0.5555 (ttp-110) cc_final: 0.4896 (mtm110) REVERT: L 53 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.6336 (ttm) REVERT: N 23 ARG cc_start: 0.7284 (mtp85) cc_final: 0.6304 (ptp-170) REVERT: N 25 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6746 (mm-30) REVERT: N 35 ARG cc_start: 0.7274 (mtt180) cc_final: 0.6313 (mtp-110) REVERT: N 61 TRP cc_start: 0.5169 (t60) cc_final: 0.4509 (p-90) REVERT: O 19 GLU cc_start: 0.7085 (mp0) cc_final: 0.6863 (mm-30) REVERT: P 48 GLU cc_start: 0.7453 (tp30) cc_final: 0.7061 (mm-30) REVERT: Q 6 GLN cc_start: 0.7604 (mp10) cc_final: 0.7163 (tt0) REVERT: Q 59 ASP cc_start: 0.8541 (m-30) cc_final: 0.8292 (m-30) REVERT: Q 82 GLU cc_start: 0.6094 (tt0) cc_final: 0.5774 (mm-30) REVERT: R 16 MET cc_start: 0.6544 (tpp) cc_final: 0.5667 (ptt) REVERT: R 81 LYS cc_start: 0.4134 (OUTLIER) cc_final: 0.1710 (pptt) REVERT: S 29 ARG cc_start: 0.6572 (mtt90) cc_final: 0.6178 (mtm110) REVERT: T 1 MET cc_start: 0.5231 (ptt) cc_final: 0.4832 (ptp) REVERT: T 3 LYS cc_start: 0.7101 (mttt) cc_final: 0.6356 (tptt) REVERT: T 23 ILE cc_start: 0.4989 (OUTLIER) cc_final: 0.4788 (tt) REVERT: T 87 ARG cc_start: 0.7055 (tpp80) cc_final: 0.6689 (ttm170) REVERT: U 21 ASN cc_start: 0.6589 (m110) cc_final: 0.6212 (m110) REVERT: U 33 LEU cc_start: 0.6643 (tp) cc_final: 0.6392 (mt) REVERT: U 41 ARG cc_start: 0.5755 (mtp180) cc_final: 0.5345 (mtt-85) REVERT: U 43 LYS cc_start: 0.6582 (mttt) cc_final: 0.6338 (mtmm) REVERT: U 47 ARG cc_start: 0.7122 (mtp85) cc_final: 0.6095 (mtm-85) REVERT: U 48 ARG cc_start: 0.6405 (OUTLIER) cc_final: 0.5823 (mtt180) REVERT: K 20 GLN cc_start: 0.6012 (mt0) cc_final: 0.5464 (tt0) REVERT: K 45 GLU cc_start: 0.6445 (mt-10) cc_final: 0.6187 (mm-30) REVERT: K 53 ARG cc_start: 0.5944 (mtm-85) cc_final: 0.5589 (ttm110) REVERT: K 57 LYS cc_start: 0.6307 (OUTLIER) cc_final: 0.6041 (tptt) REVERT: K 69 THR cc_start: 0.7322 (m) cc_final: 0.6988 (p) outliers start: 102 outliers final: 51 residues processed: 468 average time/residue: 0.7099 time to fit residues: 537.1569 Evaluate side-chains 413 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 339 time to evaluate : 3.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 86 GLN Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain U residue 20 SER Chi-restraints excluded: chain U residue 48 ARG Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 372 optimal weight: 9.9990 chunk 283 optimal weight: 8.9990 chunk 195 optimal weight: 0.0270 chunk 41 optimal weight: 10.0000 chunk 179 optimal weight: 7.9990 chunk 252 optimal weight: 7.9990 chunk 377 optimal weight: 3.9990 chunk 400 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 chunk 358 optimal weight: 0.9990 chunk 107 optimal weight: 20.0000 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 GLN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 ASN ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN R 47 HIS S 70 ASN V 40 HIS ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 55743 Z= 0.228 Angle : 0.628 8.311 81872 Z= 0.328 Chirality : 0.040 0.343 10277 Planarity : 0.005 0.053 5424 Dihedral : 23.783 179.440 24221 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.43 % Favored : 96.36 % Rotamer: Outliers : 4.79 % Allowed : 15.44 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 2884 helix: 1.15 (0.15), residues: 1164 sheet: -0.65 (0.22), residues: 500 loop : -0.90 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 200 HIS 0.006 0.001 HIS E 33 PHE 0.025 0.002 PHE H 151 TYR 0.026 0.002 TYR K 58 ARG 0.005 0.001 ARG J 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 339 time to evaluate : 3.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 MET cc_start: 0.1732 (mtt) cc_final: 0.1487 (mtm) REVERT: C 55 ILE cc_start: 0.0259 (pt) cc_final: 0.0036 (tt) REVERT: C 68 LYS cc_start: 0.3284 (mmtt) cc_final: 0.2925 (ttpt) REVERT: C 101 ASN cc_start: 0.2409 (OUTLIER) cc_final: 0.1750 (t0) REVERT: C 218 LYS cc_start: 0.5853 (tttt) cc_final: 0.5150 (tppt) REVERT: C 230 MET cc_start: 0.2834 (mmm) cc_final: 0.2616 (mtp) REVERT: C 266 ASP cc_start: 0.1822 (OUTLIER) cc_final: -0.0722 (p0) REVERT: C 323 HIS cc_start: 0.3495 (m-70) cc_final: 0.3148 (t-170) REVERT: C 346 THR cc_start: 0.5244 (m) cc_final: 0.4784 (p) REVERT: C 399 MET cc_start: 0.3673 (ptt) cc_final: 0.3225 (ptp) REVERT: C 445 GLU cc_start: 0.6365 (mp0) cc_final: 0.6142 (mp0) REVERT: C 457 GLU cc_start: 0.5878 (mt-10) cc_final: 0.5574 (tm-30) REVERT: C 466 MET cc_start: 0.4100 (ttm) cc_final: 0.3342 (mmp) REVERT: C 604 GLU cc_start: 0.5630 (tt0) cc_final: 0.4990 (tm-30) REVERT: C 613 GLU cc_start: 0.6128 (tt0) cc_final: 0.5630 (mm-30) REVERT: C 629 GLU cc_start: 0.3666 (mt-10) cc_final: 0.3295 (mm-30) REVERT: C 678 ARG cc_start: 0.2091 (ttp80) cc_final: 0.0966 (mtt90) REVERT: C 710 MET cc_start: 0.4495 (tmm) cc_final: 0.2885 (mpp) REVERT: D 21 ARG cc_start: 0.5944 (mtp-110) cc_final: 0.5704 (ttm110) REVERT: D 22 ARG cc_start: 0.6160 (OUTLIER) cc_final: 0.5384 (ttt180) REVERT: D 105 GLU cc_start: 0.6370 (mt-10) cc_final: 0.6006 (mp0) REVERT: D 108 GLN cc_start: 0.6498 (mt0) cc_final: 0.6090 (mm-40) REVERT: D 133 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.5907 (mp0) REVERT: D 142 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6469 (mm-30) REVERT: D 156 ASP cc_start: 0.5472 (p0) cc_final: 0.5264 (p0) REVERT: D 170 ARG cc_start: 0.5799 (ptt180) cc_final: 0.5361 (ptm160) REVERT: D 204 ASP cc_start: 0.5796 (OUTLIER) cc_final: 0.5175 (p0) REVERT: D 219 ASP cc_start: 0.5785 (m-30) cc_final: 0.5305 (t70) REVERT: D 223 GLU cc_start: 0.5267 (mt-10) cc_final: 0.4997 (mm-30) REVERT: E 26 LYS cc_start: 0.6018 (mttt) cc_final: 0.5148 (tmtt) REVERT: E 65 ILE cc_start: 0.6368 (OUTLIER) cc_final: 0.5909 (mt) REVERT: E 103 LEU cc_start: 0.4649 (mm) cc_final: 0.4179 (mt) REVERT: E 126 ARG cc_start: 0.4739 (mtt-85) cc_final: 0.3953 (tpp-160) REVERT: E 141 MET cc_start: 0.6256 (mmm) cc_final: 0.5712 (mmm) REVERT: E 163 ARG cc_start: 0.3615 (OUTLIER) cc_final: 0.1890 (ttt180) REVERT: E 167 TYR cc_start: 0.5338 (m-80) cc_final: 0.5104 (m-80) REVERT: E 187 GLU cc_start: 0.5285 (mt-10) cc_final: 0.4906 (pt0) REVERT: F 152 LYS cc_start: 0.6455 (mtpp) cc_final: 0.6203 (mttt) REVERT: F 178 ARG cc_start: 0.5861 (OUTLIER) cc_final: 0.5150 (ptt-90) REVERT: G 8 LYS cc_start: 0.6212 (OUTLIER) cc_final: 0.5691 (tmtt) REVERT: G 30 ARG cc_start: 0.7274 (mmm-85) cc_final: 0.6523 (tmm160) REVERT: G 88 ARG cc_start: 0.7661 (mtt-85) cc_final: 0.6868 (tmm160) REVERT: G 155 LYS cc_start: 0.7454 (ttmm) cc_final: 0.6924 (mmtm) REVERT: H 30 MET cc_start: 0.6144 (mtm) cc_final: 0.5451 (mpp) REVERT: H 60 GLU cc_start: 0.5266 (tt0) cc_final: 0.4805 (mt-10) REVERT: H 70 MET cc_start: 0.5112 (mtt) cc_final: 0.4866 (mtm) REVERT: H 94 GLU cc_start: 0.3810 (mt-10) cc_final: 0.3547 (mm-30) REVERT: I 34 ARG cc_start: 0.7183 (ttm170) cc_final: 0.6462 (ttt180) REVERT: I 38 GLU cc_start: 0.7680 (tt0) cc_final: 0.7411 (mm-30) REVERT: I 53 GLU cc_start: 0.6862 (mp0) cc_final: 0.6501 (mm-30) REVERT: I 55 SER cc_start: 0.5599 (p) cc_final: 0.5346 (m) REVERT: I 71 GLU cc_start: 0.6841 (tp30) cc_final: 0.6494 (tp30) REVERT: I 93 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6532 (mm-30) REVERT: I 110 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.6906 (mt0) REVERT: J 12 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.5494 (ttm110) REVERT: J 66 ASN cc_start: 0.5593 (t0) cc_final: 0.5201 (t0) REVERT: J 68 HIS cc_start: 0.5381 (m-70) cc_final: 0.4406 (p-80) REVERT: J 100 ARG cc_start: 0.6351 (OUTLIER) cc_final: 0.5642 (mmt90) REVERT: J 112 GLU cc_start: 0.5645 (OUTLIER) cc_final: 0.4772 (tt0) REVERT: L 17 GLU cc_start: 0.5219 (mp0) cc_final: 0.4947 (pm20) REVERT: L 32 LYS cc_start: 0.7004 (mmmt) cc_final: 0.6752 (mtpt) REVERT: L 36 THR cc_start: 0.7525 (OUTLIER) cc_final: 0.7133 (p) REVERT: N 23 ARG cc_start: 0.7383 (mtp85) cc_final: 0.6359 (ptp-170) REVERT: N 25 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6660 (mm-30) REVERT: N 35 ARG cc_start: 0.7162 (mtt180) cc_final: 0.6320 (mtp-110) REVERT: N 61 TRP cc_start: 0.5089 (t60) cc_final: 0.4423 (p-90) REVERT: O 19 GLU cc_start: 0.7165 (mp0) cc_final: 0.6937 (mm-30) REVERT: P 48 GLU cc_start: 0.7441 (tp30) cc_final: 0.7055 (mm-30) REVERT: Q 6 GLN cc_start: 0.7730 (mp10) cc_final: 0.7272 (tt0) REVERT: Q 50 ASP cc_start: 0.8199 (p0) cc_final: 0.7830 (p0) REVERT: Q 59 ASP cc_start: 0.8526 (m-30) cc_final: 0.8322 (m-30) REVERT: R 16 MET cc_start: 0.6506 (tpp) cc_final: 0.5653 (ptt) REVERT: R 52 TYR cc_start: 0.6416 (t80) cc_final: 0.6119 (t80) REVERT: R 81 LYS cc_start: 0.3784 (OUTLIER) cc_final: 0.1568 (pptt) REVERT: S 29 ARG cc_start: 0.6711 (mtt90) cc_final: 0.6378 (mtm110) REVERT: T 1 MET cc_start: 0.5167 (OUTLIER) cc_final: 0.4686 (ptp) REVERT: T 3 LYS cc_start: 0.7139 (mttt) cc_final: 0.6376 (tptt) REVERT: T 23 ILE cc_start: 0.5014 (OUTLIER) cc_final: 0.4800 (tt) REVERT: T 72 VAL cc_start: 0.5920 (t) cc_final: 0.5359 (m) REVERT: U 41 ARG cc_start: 0.5768 (mtp180) cc_final: 0.5393 (mtt-85) REVERT: U 43 LYS cc_start: 0.6725 (mttt) cc_final: 0.6435 (mtmm) REVERT: U 47 ARG cc_start: 0.7112 (mtp85) cc_final: 0.6103 (mtm-85) REVERT: U 48 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.5858 (mtt180) REVERT: V 112 ILE cc_start: 0.5711 (mm) cc_final: 0.5467 (mm) REVERT: K 20 GLN cc_start: 0.5985 (mt0) cc_final: 0.5544 (tt0) REVERT: K 45 GLU cc_start: 0.6382 (mt-10) cc_final: 0.6156 (mm-30) REVERT: K 53 ARG cc_start: 0.5973 (mtm-85) cc_final: 0.5554 (ttm110) REVERT: K 69 THR cc_start: 0.7523 (m) cc_final: 0.7167 (p) outliers start: 120 outliers final: 79 residues processed: 430 average time/residue: 0.7000 time to fit residues: 484.7122 Evaluate side-chains 411 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 314 time to evaluate : 3.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain I residue 110 GLN Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain U residue 20 SER Chi-restraints excluded: chain U residue 48 ARG Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 96 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 333 optimal weight: 6.9990 chunk 227 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 297 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 341 optimal weight: 0.1980 chunk 276 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 359 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 GLN J 5 GLN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 ASN ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN S 70 ASN V 40 HIS K 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 55743 Z= 0.226 Angle : 0.623 8.665 81872 Z= 0.324 Chirality : 0.039 0.323 10277 Planarity : 0.005 0.052 5424 Dihedral : 23.786 178.881 24217 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.50 % Favored : 96.32 % Rotamer: Outliers : 5.07 % Allowed : 15.96 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 2884 helix: 1.05 (0.15), residues: 1174 sheet: -0.59 (0.22), residues: 519 loop : -0.91 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP V 46 HIS 0.006 0.001 HIS C 656 PHE 0.021 0.002 PHE C 641 TYR 0.022 0.002 TYR K 58 ARG 0.005 0.001 ARG K 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 332 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 LYS cc_start: 0.3515 (mmtt) cc_final: 0.3136 (ttpt) REVERT: C 101 ASN cc_start: 0.2146 (OUTLIER) cc_final: 0.1570 (t0) REVERT: C 103 LEU cc_start: 0.3747 (OUTLIER) cc_final: 0.3273 (pp) REVERT: C 218 LYS cc_start: 0.5864 (tttt) cc_final: 0.5197 (tptt) REVERT: C 230 MET cc_start: 0.3048 (mmm) cc_final: 0.2763 (mtp) REVERT: C 323 HIS cc_start: 0.3428 (m-70) cc_final: 0.3091 (t-170) REVERT: C 346 THR cc_start: 0.5375 (m) cc_final: 0.4969 (p) REVERT: C 399 MET cc_start: 0.3795 (ptt) cc_final: 0.3302 (ptp) REVERT: C 445 GLU cc_start: 0.6276 (mp0) cc_final: 0.5909 (mp0) REVERT: C 457 GLU cc_start: 0.5849 (mt-10) cc_final: 0.5560 (tm-30) REVERT: C 466 MET cc_start: 0.3986 (ttm) cc_final: 0.3399 (mmp) REVERT: C 593 LEU cc_start: 0.3304 (OUTLIER) cc_final: 0.2919 (mp) REVERT: C 599 HIS cc_start: 0.6016 (OUTLIER) cc_final: 0.5623 (t70) REVERT: C 604 GLU cc_start: 0.5602 (tt0) cc_final: 0.4972 (tm-30) REVERT: C 613 GLU cc_start: 0.6062 (tt0) cc_final: 0.5649 (mm-30) REVERT: C 660 MET cc_start: 0.2900 (mmm) cc_final: 0.2609 (mmm) REVERT: C 678 ARG cc_start: 0.2016 (ttp80) cc_final: 0.1016 (ttt180) REVERT: C 710 MET cc_start: 0.4459 (tmm) cc_final: 0.2790 (mpp) REVERT: D 21 ARG cc_start: 0.5927 (mtp-110) cc_final: 0.5668 (ttm110) REVERT: D 22 ARG cc_start: 0.6219 (OUTLIER) cc_final: 0.5391 (ttt180) REVERT: D 105 GLU cc_start: 0.6472 (mt-10) cc_final: 0.6081 (mp0) REVERT: D 108 GLN cc_start: 0.6495 (mt0) cc_final: 0.6019 (mm-40) REVERT: D 133 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.5933 (mt-10) REVERT: D 142 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6485 (mm-30) REVERT: D 170 ARG cc_start: 0.5805 (ptt180) cc_final: 0.5364 (ptm160) REVERT: D 204 ASP cc_start: 0.5767 (OUTLIER) cc_final: 0.5136 (p0) REVERT: E 26 LYS cc_start: 0.5887 (mttt) cc_final: 0.4997 (tmtt) REVERT: E 65 ILE cc_start: 0.6421 (OUTLIER) cc_final: 0.5943 (mt) REVERT: E 74 MET cc_start: 0.3225 (tmm) cc_final: 0.2932 (tmm) REVERT: E 103 LEU cc_start: 0.4667 (mm) cc_final: 0.4190 (mt) REVERT: E 126 ARG cc_start: 0.4749 (mtt-85) cc_final: 0.3893 (tpp-160) REVERT: E 163 ARG cc_start: 0.3522 (OUTLIER) cc_final: 0.1722 (ttt180) REVERT: F 54 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.6700 (tmmm) REVERT: F 152 LYS cc_start: 0.6390 (mtpp) cc_final: 0.6140 (mttt) REVERT: F 178 ARG cc_start: 0.5741 (OUTLIER) cc_final: 0.5091 (ptt-90) REVERT: G 8 LYS cc_start: 0.6194 (OUTLIER) cc_final: 0.5681 (tmtt) REVERT: G 30 ARG cc_start: 0.7253 (mmm-85) cc_final: 0.6509 (tmm160) REVERT: G 155 LYS cc_start: 0.7408 (ttmm) cc_final: 0.6863 (mmtm) REVERT: H 30 MET cc_start: 0.6068 (mtm) cc_final: 0.5134 (mpp) REVERT: H 60 GLU cc_start: 0.5449 (tt0) cc_final: 0.4964 (mt-10) REVERT: H 70 MET cc_start: 0.4930 (mtt) cc_final: 0.4722 (mtp) REVERT: H 94 GLU cc_start: 0.3590 (mt-10) cc_final: 0.3382 (mm-30) REVERT: I 34 ARG cc_start: 0.7095 (ttm170) cc_final: 0.6531 (ttt180) REVERT: I 54 ASP cc_start: 0.7222 (m-30) cc_final: 0.6576 (p0) REVERT: I 55 SER cc_start: 0.5539 (p) cc_final: 0.5054 (m) REVERT: I 110 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.6863 (mt0) REVERT: J 12 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.5610 (ttm110) REVERT: J 66 ASN cc_start: 0.5541 (t0) cc_final: 0.5071 (t0) REVERT: J 68 HIS cc_start: 0.5385 (m-70) cc_final: 0.4408 (p-80) REVERT: J 100 ARG cc_start: 0.6289 (OUTLIER) cc_final: 0.5594 (mmt90) REVERT: J 112 GLU cc_start: 0.5532 (OUTLIER) cc_final: 0.4689 (tt0) REVERT: L 17 GLU cc_start: 0.5406 (mp0) cc_final: 0.4919 (pm20) REVERT: L 32 LYS cc_start: 0.6960 (mmmt) cc_final: 0.6720 (mtpt) REVERT: L 36 THR cc_start: 0.7525 (OUTLIER) cc_final: 0.7174 (p) REVERT: N 23 ARG cc_start: 0.7321 (mtp85) cc_final: 0.6172 (ptp-170) REVERT: N 25 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6577 (mm-30) REVERT: N 35 ARG cc_start: 0.7127 (mtt180) cc_final: 0.6311 (mtp-110) REVERT: N 61 TRP cc_start: 0.4952 (t60) cc_final: 0.4255 (p-90) REVERT: O 19 GLU cc_start: 0.7100 (mp0) cc_final: 0.6887 (mm-30) REVERT: P 48 GLU cc_start: 0.7529 (tp30) cc_final: 0.7082 (mm-30) REVERT: Q 6 GLN cc_start: 0.7777 (mp10) cc_final: 0.7308 (tt0) REVERT: Q 50 ASP cc_start: 0.8187 (p0) cc_final: 0.7801 (p0) REVERT: R 16 MET cc_start: 0.6546 (tpp) cc_final: 0.5727 (ptt) REVERT: R 52 TYR cc_start: 0.6384 (t80) cc_final: 0.5897 (t80) REVERT: R 81 LYS cc_start: 0.3670 (OUTLIER) cc_final: 0.1839 (tptt) REVERT: S 29 ARG cc_start: 0.6660 (mtt90) cc_final: 0.6295 (mtm110) REVERT: S 34 GLN cc_start: 0.6466 (tp-100) cc_final: 0.6182 (tt0) REVERT: T 1 MET cc_start: 0.5114 (OUTLIER) cc_final: 0.4659 (ptp) REVERT: T 3 LYS cc_start: 0.7149 (mttt) cc_final: 0.6410 (tptt) REVERT: T 10 ILE cc_start: 0.6800 (mt) cc_final: 0.6364 (mm) REVERT: T 23 ILE cc_start: 0.4846 (OUTLIER) cc_final: 0.4618 (tt) REVERT: T 72 VAL cc_start: 0.5913 (t) cc_final: 0.5282 (m) REVERT: U 41 ARG cc_start: 0.5834 (mtp180) cc_final: 0.5435 (mtt-85) REVERT: U 43 LYS cc_start: 0.6699 (mttt) cc_final: 0.6437 (mtmm) REVERT: U 47 ARG cc_start: 0.7099 (mtp85) cc_final: 0.5890 (mtm-85) REVERT: U 48 ARG cc_start: 0.6727 (mtm110) cc_final: 0.5757 (mtt180) REVERT: V 112 ILE cc_start: 0.5811 (mm) cc_final: 0.5443 (mm) REVERT: K 20 GLN cc_start: 0.5980 (mt0) cc_final: 0.5554 (tt0) REVERT: K 45 GLU cc_start: 0.6363 (mt-10) cc_final: 0.6144 (mm-30) REVERT: K 53 ARG cc_start: 0.5924 (mtm-85) cc_final: 0.5502 (ttm110) REVERT: K 69 THR cc_start: 0.7517 (m) cc_final: 0.7199 (p) outliers start: 127 outliers final: 82 residues processed: 429 average time/residue: 0.6860 time to fit residues: 476.9223 Evaluate side-chains 411 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 309 time to evaluate : 3.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 599 HIS Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 110 GLN Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 96 GLU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 96 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 134 optimal weight: 0.0980 chunk 360 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 234 optimal weight: 10.0000 chunk 98 optimal weight: 30.0000 chunk 400 optimal weight: 5.9990 chunk 332 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 210 optimal weight: 8.9990 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 HIS E 113 GLN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN J 5 GLN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 ASN ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 70 ASN V 40 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 55743 Z= 0.359 Angle : 0.772 9.999 81872 Z= 0.395 Chirality : 0.046 0.358 10277 Planarity : 0.006 0.056 5424 Dihedral : 24.020 178.368 24210 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.40 % Favored : 95.42 % Rotamer: Outliers : 5.50 % Allowed : 17.11 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.15), residues: 2884 helix: 0.51 (0.15), residues: 1162 sheet: -0.68 (0.22), residues: 496 loop : -1.23 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP E 200 HIS 0.008 0.002 HIS C 569 PHE 0.034 0.003 PHE C 641 TYR 0.021 0.003 TYR K 58 ARG 0.016 0.001 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 321 time to evaluate : 3.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 ARG cc_start: 0.2811 (mtt-85) cc_final: 0.2193 (ppt170) REVERT: C 68 LYS cc_start: 0.3479 (mmtt) cc_final: 0.3053 (ttpt) REVERT: C 101 ASN cc_start: 0.2555 (OUTLIER) cc_final: 0.1883 (t0) REVERT: C 102 GLU cc_start: 0.1372 (OUTLIER) cc_final: 0.0930 (mp0) REVERT: C 103 LEU cc_start: 0.3667 (OUTLIER) cc_final: 0.3237 (pp) REVERT: C 218 LYS cc_start: 0.5730 (tttt) cc_final: 0.4940 (tppt) REVERT: C 230 MET cc_start: 0.2925 (mmm) cc_final: 0.2653 (mtp) REVERT: C 252 ARG cc_start: 0.4534 (mtm110) cc_final: 0.3888 (ttm170) REVERT: C 255 VAL cc_start: 0.4302 (t) cc_final: 0.3917 (p) REVERT: C 266 ASP cc_start: 0.1765 (OUTLIER) cc_final: -0.0796 (p0) REVERT: C 301 ASP cc_start: 0.4520 (t70) cc_final: 0.4282 (t0) REVERT: C 323 HIS cc_start: 0.3653 (m-70) cc_final: 0.3310 (t-170) REVERT: C 346 THR cc_start: 0.5317 (m) cc_final: 0.4931 (p) REVERT: C 399 MET cc_start: 0.3928 (ptt) cc_final: 0.3483 (ptp) REVERT: C 430 GLU cc_start: 0.3588 (mp0) cc_final: 0.3076 (tt0) REVERT: C 445 GLU cc_start: 0.6158 (mp0) cc_final: 0.5903 (mp0) REVERT: C 457 GLU cc_start: 0.5792 (mt-10) cc_final: 0.5492 (tm-30) REVERT: C 466 MET cc_start: 0.4126 (ttm) cc_final: 0.3582 (mmp) REVERT: C 595 ASP cc_start: 0.4354 (OUTLIER) cc_final: 0.4055 (t0) REVERT: C 599 HIS cc_start: 0.5869 (OUTLIER) cc_final: 0.5483 (t70) REVERT: C 604 GLU cc_start: 0.5614 (tt0) cc_final: 0.4958 (tm-30) REVERT: C 613 GLU cc_start: 0.6164 (tt0) cc_final: 0.5784 (mm-30) REVERT: C 660 MET cc_start: 0.2969 (mmm) cc_final: 0.2619 (mmm) REVERT: C 669 GLU cc_start: 0.5653 (tt0) cc_final: 0.5349 (mp0) REVERT: C 678 ARG cc_start: 0.1930 (ttp80) cc_final: 0.0957 (ttt180) REVERT: D 21 ARG cc_start: 0.5869 (mtp-110) cc_final: 0.5662 (ttm110) REVERT: D 22 ARG cc_start: 0.6361 (OUTLIER) cc_final: 0.5409 (ttt180) REVERT: D 34 GLU cc_start: 0.6556 (pt0) cc_final: 0.5943 (pp20) REVERT: D 105 GLU cc_start: 0.6523 (mt-10) cc_final: 0.6081 (mp0) REVERT: D 108 GLN cc_start: 0.6482 (mt0) cc_final: 0.6117 (mm110) REVERT: D 133 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.5987 (mp0) REVERT: D 142 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6500 (mm-30) REVERT: D 170 ARG cc_start: 0.5889 (ptt180) cc_final: 0.5430 (ptm160) REVERT: D 204 ASP cc_start: 0.5920 (OUTLIER) cc_final: 0.5266 (p0) REVERT: E 26 LYS cc_start: 0.5860 (mttt) cc_final: 0.5212 (ttmt) REVERT: E 65 ILE cc_start: 0.6424 (OUTLIER) cc_final: 0.5956 (mt) REVERT: E 74 MET cc_start: 0.3106 (tmm) cc_final: 0.2829 (tmm) REVERT: E 126 ARG cc_start: 0.4903 (mtt-85) cc_final: 0.4019 (tpp-160) REVERT: E 163 ARG cc_start: 0.3531 (OUTLIER) cc_final: 0.1704 (ttt180) REVERT: F 54 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.6808 (tmmm) REVERT: F 152 LYS cc_start: 0.6455 (mtpp) cc_final: 0.6163 (mttt) REVERT: F 178 ARG cc_start: 0.6123 (OUTLIER) cc_final: 0.5366 (ptt-90) REVERT: G 8 LYS cc_start: 0.6142 (OUTLIER) cc_final: 0.5620 (tmtt) REVERT: G 30 ARG cc_start: 0.7249 (mmm-85) cc_final: 0.6450 (tmm160) REVERT: G 155 LYS cc_start: 0.7476 (ttmm) cc_final: 0.7095 (ttpt) REVERT: H 13 LEU cc_start: 0.4945 (OUTLIER) cc_final: 0.4728 (mm) REVERT: H 30 MET cc_start: 0.5943 (mtm) cc_final: 0.5280 (mpp) REVERT: H 60 GLU cc_start: 0.5424 (tt0) cc_final: 0.4909 (mt-10) REVERT: H 70 MET cc_start: 0.4947 (mtt) cc_final: 0.4708 (mtm) REVERT: I 34 ARG cc_start: 0.7102 (ttm170) cc_final: 0.6520 (ttt180) REVERT: I 55 SER cc_start: 0.5535 (p) cc_final: 0.5231 (m) REVERT: I 110 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.6912 (mt0) REVERT: J 12 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.5740 (ttm110) REVERT: J 66 ASN cc_start: 0.5713 (t0) cc_final: 0.5343 (t0) REVERT: J 68 HIS cc_start: 0.5658 (m-70) cc_final: 0.4762 (p-80) REVERT: J 112 GLU cc_start: 0.5486 (OUTLIER) cc_final: 0.4650 (tt0) REVERT: L 17 GLU cc_start: 0.5595 (mp0) cc_final: 0.5099 (pm20) REVERT: L 32 LYS cc_start: 0.6967 (mmmt) cc_final: 0.6710 (mtpt) REVERT: L 36 THR cc_start: 0.7559 (OUTLIER) cc_final: 0.7227 (p) REVERT: N 35 ARG cc_start: 0.6984 (mtt180) cc_final: 0.6231 (mtp-110) REVERT: N 61 TRP cc_start: 0.4936 (OUTLIER) cc_final: 0.4192 (p-90) REVERT: Q 3 GLU cc_start: 0.6080 (mm-30) cc_final: 0.5330 (mt-10) REVERT: R 16 MET cc_start: 0.6604 (tpp) cc_final: 0.5814 (ptt) REVERT: R 52 TYR cc_start: 0.6425 (t80) cc_final: 0.6053 (t80) REVERT: R 73 GLU cc_start: 0.5555 (mt-10) cc_final: 0.4970 (tp30) REVERT: S 16 GLU cc_start: 0.7830 (mt-10) cc_final: 0.6815 (tm-30) REVERT: S 29 ARG cc_start: 0.6673 (mtt90) cc_final: 0.6338 (mtm110) REVERT: T 1 MET cc_start: 0.5294 (OUTLIER) cc_final: 0.4905 (ptp) REVERT: T 3 LYS cc_start: 0.6987 (mttt) cc_final: 0.6281 (tptt) REVERT: T 10 ILE cc_start: 0.6793 (mt) cc_final: 0.6361 (mm) REVERT: T 23 ILE cc_start: 0.4877 (OUTLIER) cc_final: 0.4616 (tt) REVERT: T 33 ASN cc_start: 0.5855 (m110) cc_final: 0.5283 (t0) REVERT: T 72 VAL cc_start: 0.6022 (OUTLIER) cc_final: 0.5560 (m) REVERT: U 41 ARG cc_start: 0.5856 (mtp180) cc_final: 0.5462 (mtt-85) REVERT: U 47 ARG cc_start: 0.7109 (mtp85) cc_final: 0.5878 (mtm-85) REVERT: U 48 ARG cc_start: 0.6696 (mtm110) cc_final: 0.5677 (mtt180) REVERT: V 19 GLU cc_start: 0.5339 (mt-10) cc_final: 0.4820 (mp0) REVERT: V 112 ILE cc_start: 0.5540 (mm) cc_final: 0.5143 (mm) REVERT: K 20 GLN cc_start: 0.6126 (mt0) cc_final: 0.5605 (tt0) REVERT: K 45 GLU cc_start: 0.6305 (mt-10) cc_final: 0.6104 (mm-30) REVERT: K 53 ARG cc_start: 0.5885 (mtm-85) cc_final: 0.5470 (ttm110) REVERT: K 57 LYS cc_start: 0.6513 (OUTLIER) cc_final: 0.5372 (tmtm) REVERT: K 69 THR cc_start: 0.7592 (m) cc_final: 0.7385 (p) outliers start: 138 outliers final: 96 residues processed: 429 average time/residue: 0.6862 time to fit residues: 483.4596 Evaluate side-chains 422 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 302 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 599 HIS Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 110 GLN Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain N residue 61 TRP Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 9 ILE Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 35 THR Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 96 GLU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 96 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 386 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 228 optimal weight: 0.9990 chunk 292 optimal weight: 1.9990 chunk 226 optimal weight: 10.0000 chunk 337 optimal weight: 0.4980 chunk 223 optimal weight: 0.9990 chunk 399 optimal weight: 8.9990 chunk 249 optimal weight: 0.6980 chunk 243 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 464 HIS D 123 ASN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 ASN Q 54 GLN ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 ASN S 70 ASN V 40 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 55743 Z= 0.143 Angle : 0.567 9.020 81872 Z= 0.295 Chirality : 0.036 0.279 10277 Planarity : 0.004 0.046 5424 Dihedral : 23.738 179.213 24210 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.46 % Favored : 97.40 % Rotamer: Outliers : 3.71 % Allowed : 19.31 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 2884 helix: 1.09 (0.15), residues: 1181 sheet: -0.42 (0.22), residues: 514 loop : -0.90 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP V 46 HIS 0.006 0.001 HIS V 40 PHE 0.026 0.001 PHE T 26 TYR 0.018 0.001 TYR K 58 ARG 0.007 0.000 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 341 time to evaluate : 3.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 LYS cc_start: 0.3451 (mmtt) cc_final: 0.3052 (ttpt) REVERT: C 101 ASN cc_start: 0.2361 (OUTLIER) cc_final: 0.1563 (t0) REVERT: C 103 LEU cc_start: 0.3507 (OUTLIER) cc_final: 0.3118 (pp) REVERT: C 218 LYS cc_start: 0.5817 (tttt) cc_final: 0.5166 (tptt) REVERT: C 230 MET cc_start: 0.3103 (mmm) cc_final: 0.2793 (mtp) REVERT: C 252 ARG cc_start: 0.4857 (mtm110) cc_final: 0.4087 (ttm170) REVERT: C 277 ASP cc_start: 0.4664 (m-30) cc_final: 0.4141 (t0) REVERT: C 346 THR cc_start: 0.5487 (m) cc_final: 0.5086 (p) REVERT: C 399 MET cc_start: 0.3884 (ptt) cc_final: 0.3438 (ptp) REVERT: C 430 GLU cc_start: 0.3753 (mp0) cc_final: 0.3235 (tt0) REVERT: C 439 ARG cc_start: 0.4033 (ttt-90) cc_final: 0.3195 (ttp-170) REVERT: C 445 GLU cc_start: 0.6245 (mp0) cc_final: 0.5887 (mp0) REVERT: C 457 GLU cc_start: 0.5849 (mt-10) cc_final: 0.5550 (tm-30) REVERT: C 466 MET cc_start: 0.4288 (ttm) cc_final: 0.3511 (mmp) REVERT: C 526 SER cc_start: 0.6330 (m) cc_final: 0.5870 (p) REVERT: C 531 ARG cc_start: 0.4334 (mtt180) cc_final: 0.3986 (mmt180) REVERT: C 593 LEU cc_start: 0.3266 (OUTLIER) cc_final: 0.2913 (mp) REVERT: C 604 GLU cc_start: 0.5726 (tt0) cc_final: 0.5079 (tm-30) REVERT: C 613 GLU cc_start: 0.6055 (tt0) cc_final: 0.5596 (mm-30) REVERT: C 678 ARG cc_start: 0.1740 (ttp80) cc_final: 0.0963 (ttt180) REVERT: C 710 MET cc_start: 0.4390 (tmm) cc_final: 0.2840 (mpp) REVERT: D 21 ARG cc_start: 0.5857 (mtp-110) cc_final: 0.5637 (ttm110) REVERT: D 22 ARG cc_start: 0.6250 (OUTLIER) cc_final: 0.5408 (ttt180) REVERT: D 34 GLU cc_start: 0.6498 (pt0) cc_final: 0.5684 (pp20) REVERT: D 105 GLU cc_start: 0.6553 (mt-10) cc_final: 0.6198 (mp0) REVERT: D 108 GLN cc_start: 0.6488 (mt0) cc_final: 0.6106 (mm110) REVERT: D 142 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6524 (mm-30) REVERT: D 170 ARG cc_start: 0.5730 (ptt180) cc_final: 0.5275 (ptm160) REVERT: D 204 ASP cc_start: 0.5671 (OUTLIER) cc_final: 0.5057 (p0) REVERT: E 26 LYS cc_start: 0.5891 (mttt) cc_final: 0.4860 (tptt) REVERT: E 65 ILE cc_start: 0.6405 (OUTLIER) cc_final: 0.5931 (mt) REVERT: E 74 MET cc_start: 0.3242 (tmm) cc_final: 0.3011 (tmm) REVERT: E 99 HIS cc_start: 0.5507 (OUTLIER) cc_final: 0.5070 (m-70) REVERT: E 103 LEU cc_start: 0.4694 (mm) cc_final: 0.4201 (mt) REVERT: E 126 ARG cc_start: 0.4823 (mtt-85) cc_final: 0.3931 (tpp-160) REVERT: E 163 ARG cc_start: 0.3592 (OUTLIER) cc_final: 0.1750 (ttt180) REVERT: F 54 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.6577 (tmmm) REVERT: G 8 LYS cc_start: 0.6252 (OUTLIER) cc_final: 0.5768 (tmtt) REVERT: G 30 ARG cc_start: 0.7258 (mmm-85) cc_final: 0.6536 (tmm160) REVERT: G 88 ARG cc_start: 0.7619 (mtt-85) cc_final: 0.6892 (ttp-170) REVERT: G 149 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.7116 (mtt90) REVERT: G 152 ASP cc_start: 0.6385 (m-30) cc_final: 0.5917 (t0) REVERT: G 155 LYS cc_start: 0.7428 (ttmm) cc_final: 0.7035 (ttpt) REVERT: H 9 LYS cc_start: 0.4764 (mmtt) cc_final: 0.4277 (pttp) REVERT: H 13 LEU cc_start: 0.5067 (OUTLIER) cc_final: 0.4836 (mm) REVERT: H 30 MET cc_start: 0.5740 (mtm) cc_final: 0.5191 (mpp) REVERT: H 60 GLU cc_start: 0.5244 (tt0) cc_final: 0.4734 (mt-10) REVERT: H 70 MET cc_start: 0.5052 (mtt) cc_final: 0.4687 (mtp) REVERT: H 86 GLN cc_start: 0.3869 (mm-40) cc_final: 0.3634 (mp10) REVERT: H 138 ARG cc_start: 0.3607 (tmm160) cc_final: 0.3166 (tmm160) REVERT: I 34 ARG cc_start: 0.7160 (ttm170) cc_final: 0.6586 (ttt180) REVERT: I 54 ASP cc_start: 0.7248 (m-30) cc_final: 0.6574 (p0) REVERT: I 55 SER cc_start: 0.5492 (p) cc_final: 0.4997 (m) REVERT: J 12 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.5671 (ttm110) REVERT: J 66 ASN cc_start: 0.5433 (t0) cc_final: 0.5027 (t0) REVERT: J 68 HIS cc_start: 0.5563 (m-70) cc_final: 0.4637 (p-80) REVERT: J 100 ARG cc_start: 0.6279 (OUTLIER) cc_final: 0.5902 (mmt-90) REVERT: J 112 GLU cc_start: 0.5578 (OUTLIER) cc_final: 0.4700 (tt0) REVERT: L 17 GLU cc_start: 0.5683 (mp0) cc_final: 0.4979 (pm20) REVERT: L 32 LYS cc_start: 0.6950 (mmmt) cc_final: 0.6712 (mtpt) REVERT: L 36 THR cc_start: 0.7599 (OUTLIER) cc_final: 0.7284 (p) REVERT: M 14 ARG cc_start: 0.3633 (ttm170) cc_final: 0.2801 (mtp-110) REVERT: N 35 ARG cc_start: 0.7241 (mtt180) cc_final: 0.6316 (mtp-110) REVERT: O 19 GLU cc_start: 0.7116 (mp0) cc_final: 0.6912 (mm-30) REVERT: Q 3 GLU cc_start: 0.6115 (mm-30) cc_final: 0.5403 (mt-10) REVERT: R 16 MET cc_start: 0.6582 (tpp) cc_final: 0.5782 (ptt) REVERT: R 52 TYR cc_start: 0.6291 (t80) cc_final: 0.5962 (t80) REVERT: R 73 GLU cc_start: 0.5562 (mt-10) cc_final: 0.4960 (tp30) REVERT: S 29 ARG cc_start: 0.6690 (mtt90) cc_final: 0.6316 (mtm110) REVERT: S 34 GLN cc_start: 0.6449 (tp-100) cc_final: 0.6147 (tt0) REVERT: T 1 MET cc_start: 0.5107 (OUTLIER) cc_final: 0.4467 (ptp) REVERT: T 3 LYS cc_start: 0.7051 (mttt) cc_final: 0.6334 (tptt) REVERT: T 10 ILE cc_start: 0.6786 (mt) cc_final: 0.6221 (mm) REVERT: T 23 ILE cc_start: 0.4584 (OUTLIER) cc_final: 0.4327 (tt) REVERT: T 36 GLU cc_start: 0.5700 (pt0) cc_final: 0.5207 (pm20) REVERT: T 72 VAL cc_start: 0.5759 (t) cc_final: 0.5212 (m) REVERT: T 84 ASP cc_start: 0.4708 (m-30) cc_final: 0.4331 (t0) REVERT: U 41 ARG cc_start: 0.5936 (mtp180) cc_final: 0.5429 (mtt-85) REVERT: U 47 ARG cc_start: 0.7002 (mtp85) cc_final: 0.5898 (mtm-85) REVERT: U 48 ARG cc_start: 0.6681 (mtm110) cc_final: 0.5644 (mtt180) REVERT: V 19 GLU cc_start: 0.5226 (mt-10) cc_final: 0.4676 (mp0) REVERT: V 112 ILE cc_start: 0.5506 (mm) cc_final: 0.5107 (mm) REVERT: K 20 GLN cc_start: 0.5979 (mt0) cc_final: 0.5491 (tt0) REVERT: K 45 GLU cc_start: 0.6359 (mt-10) cc_final: 0.6147 (mm-30) REVERT: K 53 ARG cc_start: 0.5763 (mtm-85) cc_final: 0.5400 (ttm110) REVERT: K 57 LYS cc_start: 0.6464 (OUTLIER) cc_final: 0.6088 (tptt) REVERT: K 69 THR cc_start: 0.7465 (m) cc_final: 0.7208 (p) outliers start: 93 outliers final: 59 residues processed: 410 average time/residue: 0.6970 time to fit residues: 463.4094 Evaluate side-chains 390 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 312 time to evaluate : 3.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 96 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 246 optimal weight: 9.9990 chunk 159 optimal weight: 0.0000 chunk 238 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 253 optimal weight: 5.9990 chunk 271 optimal weight: 2.9990 chunk 197 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 313 optimal weight: 9.9990 overall best weight: 5.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 464 HIS E 113 GLN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 ASN Q 52 ASN ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 70 ASN V 30 ASN V 40 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 55743 Z= 0.342 Angle : 0.735 9.686 81872 Z= 0.375 Chirality : 0.044 0.342 10277 Planarity : 0.006 0.052 5424 Dihedral : 23.900 178.760 24206 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.40 % Favored : 95.46 % Rotamer: Outliers : 5.07 % Allowed : 18.59 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 2884 helix: 0.62 (0.15), residues: 1184 sheet: -0.58 (0.22), residues: 497 loop : -1.17 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 200 HIS 0.007 0.002 HIS R 14 PHE 0.030 0.003 PHE C 641 TYR 0.028 0.002 TYR K 58 ARG 0.007 0.001 ARG J 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 302 time to evaluate : 3.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 LYS cc_start: 0.3444 (mmtt) cc_final: 0.2983 (ttpt) REVERT: C 101 ASN cc_start: 0.2569 (OUTLIER) cc_final: 0.1765 (t0) REVERT: C 103 LEU cc_start: 0.3659 (OUTLIER) cc_final: 0.3170 (pp) REVERT: C 113 MET cc_start: 0.4461 (ptt) cc_final: 0.3777 (mtm) REVERT: C 131 ARG cc_start: 0.5738 (ttt180) cc_final: 0.3352 (tpt90) REVERT: C 218 LYS cc_start: 0.5753 (tttt) cc_final: 0.5042 (tptt) REVERT: C 230 MET cc_start: 0.3030 (mmm) cc_final: 0.2726 (mtp) REVERT: C 252 ARG cc_start: 0.4449 (mtm110) cc_final: 0.3825 (ttt-90) REVERT: C 266 ASP cc_start: 0.1739 (OUTLIER) cc_final: -0.0898 (p0) REVERT: C 323 HIS cc_start: 0.3530 (m-70) cc_final: 0.3189 (t-170) REVERT: C 399 MET cc_start: 0.4191 (ptt) cc_final: 0.3734 (ptp) REVERT: C 430 GLU cc_start: 0.3609 (mp0) cc_final: 0.3106 (tt0) REVERT: C 445 GLU cc_start: 0.6260 (mp0) cc_final: 0.6013 (mp0) REVERT: C 457 GLU cc_start: 0.5817 (mt-10) cc_final: 0.5511 (tm-30) REVERT: C 466 MET cc_start: 0.3980 (ttm) cc_final: 0.3463 (mmp) REVERT: C 593 LEU cc_start: 0.3293 (OUTLIER) cc_final: 0.2945 (mp) REVERT: C 599 HIS cc_start: 0.5869 (OUTLIER) cc_final: 0.5520 (t70) REVERT: C 604 GLU cc_start: 0.5645 (tt0) cc_final: 0.4998 (tm-30) REVERT: C 613 GLU cc_start: 0.6217 (tt0) cc_final: 0.5805 (mm-30) REVERT: C 669 GLU cc_start: 0.5606 (tt0) cc_final: 0.5331 (mp0) REVERT: C 678 ARG cc_start: 0.1783 (ttp80) cc_final: 0.1030 (ttt180) REVERT: D 22 ARG cc_start: 0.6359 (OUTLIER) cc_final: 0.5425 (ttt180) REVERT: D 34 GLU cc_start: 0.6586 (pt0) cc_final: 0.5969 (pp20) REVERT: D 105 GLU cc_start: 0.6571 (mt-10) cc_final: 0.6178 (mp0) REVERT: D 108 GLN cc_start: 0.6477 (mt0) cc_final: 0.6108 (mm110) REVERT: D 133 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6029 (mt-10) REVERT: D 142 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6526 (mm-30) REVERT: D 170 ARG cc_start: 0.5908 (ptt180) cc_final: 0.5436 (ptm160) REVERT: D 204 ASP cc_start: 0.5771 (OUTLIER) cc_final: 0.5120 (p0) REVERT: E 26 LYS cc_start: 0.5883 (mttt) cc_final: 0.4964 (tmtt) REVERT: E 65 ILE cc_start: 0.6442 (OUTLIER) cc_final: 0.5961 (mt) REVERT: E 74 MET cc_start: 0.3148 (tmm) cc_final: 0.2898 (tmm) REVERT: E 99 HIS cc_start: 0.5575 (OUTLIER) cc_final: 0.4848 (m-70) REVERT: E 126 ARG cc_start: 0.4970 (mtt-85) cc_final: 0.4093 (tpp-160) REVERT: E 163 ARG cc_start: 0.3617 (ppt170) cc_final: 0.1759 (ttt180) REVERT: F 54 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.6771 (tmmm) REVERT: G 8 LYS cc_start: 0.6172 (OUTLIER) cc_final: 0.5641 (tmtt) REVERT: G 30 ARG cc_start: 0.7255 (mmm-85) cc_final: 0.6476 (tmm160) REVERT: G 155 LYS cc_start: 0.7481 (ttmm) cc_final: 0.7102 (ttpt) REVERT: H 13 LEU cc_start: 0.4989 (OUTLIER) cc_final: 0.4778 (mm) REVERT: H 60 GLU cc_start: 0.5389 (tt0) cc_final: 0.4890 (mt-10) REVERT: I 34 ARG cc_start: 0.7103 (ttm170) cc_final: 0.6532 (ttt180) REVERT: I 54 ASP cc_start: 0.7221 (m-30) cc_final: 0.6500 (p0) REVERT: I 55 SER cc_start: 0.5537 (p) cc_final: 0.4949 (m) REVERT: I 110 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.6882 (mm-40) REVERT: J 12 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.5772 (ttm110) REVERT: J 66 ASN cc_start: 0.5618 (t0) cc_final: 0.5271 (t0) REVERT: J 68 HIS cc_start: 0.5606 (m-70) cc_final: 0.4744 (p-80) REVERT: J 112 GLU cc_start: 0.5548 (OUTLIER) cc_final: 0.4696 (tt0) REVERT: L 17 GLU cc_start: 0.5645 (mp0) cc_final: 0.5056 (pm20) REVERT: L 32 LYS cc_start: 0.6975 (mmmt) cc_final: 0.6732 (mtpt) REVERT: L 36 THR cc_start: 0.7525 (OUTLIER) cc_final: 0.7205 (p) REVERT: N 35 ARG cc_start: 0.7064 (mtt180) cc_final: 0.6266 (mtp-110) REVERT: Q 3 GLU cc_start: 0.6039 (mm-30) cc_final: 0.5318 (mt-10) REVERT: Q 50 ASP cc_start: 0.8350 (p0) cc_final: 0.8082 (p0) REVERT: R 16 MET cc_start: 0.6659 (tpp) cc_final: 0.5821 (ptt) REVERT: R 52 TYR cc_start: 0.6207 (t80) cc_final: 0.5869 (t80) REVERT: R 73 GLU cc_start: 0.5322 (mt-10) cc_final: 0.4826 (tp30) REVERT: S 16 GLU cc_start: 0.7787 (mt-10) cc_final: 0.6795 (tm-30) REVERT: S 29 ARG cc_start: 0.6726 (mtt90) cc_final: 0.6412 (mtm110) REVERT: T 1 MET cc_start: 0.5310 (OUTLIER) cc_final: 0.4714 (ptp) REVERT: T 3 LYS cc_start: 0.6988 (mttt) cc_final: 0.6289 (tptt) REVERT: T 10 ILE cc_start: 0.6805 (mt) cc_final: 0.6260 (mm) REVERT: T 23 ILE cc_start: 0.4685 (OUTLIER) cc_final: 0.4393 (tt) REVERT: T 33 ASN cc_start: 0.5663 (m110) cc_final: 0.5330 (p0) REVERT: T 36 GLU cc_start: 0.5842 (pt0) cc_final: 0.5332 (pm20) REVERT: T 72 VAL cc_start: 0.5866 (OUTLIER) cc_final: 0.5369 (m) REVERT: T 84 ASP cc_start: 0.4790 (m-30) cc_final: 0.4334 (t0) REVERT: U 41 ARG cc_start: 0.5925 (mtp180) cc_final: 0.5414 (mtt-85) REVERT: U 47 ARG cc_start: 0.7078 (mtp85) cc_final: 0.6015 (mtm-85) REVERT: U 48 ARG cc_start: 0.6684 (mtm110) cc_final: 0.5648 (mtt180) REVERT: V 19 GLU cc_start: 0.5300 (mt-10) cc_final: 0.4761 (mp0) REVERT: K 20 GLN cc_start: 0.6134 (mt0) cc_final: 0.5615 (tt0) REVERT: K 53 ARG cc_start: 0.5808 (mtm-85) cc_final: 0.5394 (ttm110) REVERT: K 57 LYS cc_start: 0.6527 (OUTLIER) cc_final: 0.5312 (tmtm) REVERT: K 69 THR cc_start: 0.7575 (m) cc_final: 0.7337 (p) outliers start: 127 outliers final: 87 residues processed: 404 average time/residue: 0.6840 time to fit residues: 449.2010 Evaluate side-chains 397 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 289 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 599 HIS Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 110 GLN Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain N residue 61 TRP Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 76 ASP Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 96 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 362 optimal weight: 4.9990 chunk 382 optimal weight: 0.6980 chunk 348 optimal weight: 5.9990 chunk 371 optimal weight: 9.9990 chunk 223 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 291 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 336 optimal weight: 5.9990 chunk 351 optimal weight: 1.9990 chunk 370 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 464 HIS ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 70 ASN V 40 HIS V 79 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 55743 Z= 0.175 Angle : 0.587 9.354 81872 Z= 0.305 Chirality : 0.037 0.291 10277 Planarity : 0.004 0.051 5424 Dihedral : 23.744 179.882 24202 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.05 % Favored : 96.81 % Rotamer: Outliers : 3.79 % Allowed : 20.22 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 2884 helix: 0.95 (0.15), residues: 1179 sheet: -0.50 (0.22), residues: 504 loop : -0.97 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 200 HIS 0.007 0.001 HIS V 40 PHE 0.024 0.002 PHE C 470 TYR 0.020 0.001 TYR K 58 ARG 0.007 0.000 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 320 time to evaluate : 3.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 LYS cc_start: 0.3409 (mmtt) cc_final: 0.3042 (ttpt) REVERT: C 101 ASN cc_start: 0.2505 (OUTLIER) cc_final: 0.1539 (t0) REVERT: C 103 LEU cc_start: 0.3666 (OUTLIER) cc_final: 0.3156 (pp) REVERT: C 131 ARG cc_start: 0.5622 (ttt180) cc_final: 0.3546 (tpt90) REVERT: C 218 LYS cc_start: 0.5804 (tttt) cc_final: 0.5085 (tptt) REVERT: C 230 MET cc_start: 0.3069 (mmm) cc_final: 0.2663 (mtp) REVERT: C 266 ASP cc_start: 0.1689 (OUTLIER) cc_final: -0.1104 (p0) REVERT: C 277 ASP cc_start: 0.4610 (m-30) cc_final: 0.4096 (t0) REVERT: C 323 HIS cc_start: 0.3423 (m-70) cc_final: 0.3132 (t-170) REVERT: C 346 THR cc_start: 0.5578 (m) cc_final: 0.5303 (p) REVERT: C 399 MET cc_start: 0.4128 (ptt) cc_final: 0.3676 (ptp) REVERT: C 430 GLU cc_start: 0.3915 (mp0) cc_final: 0.3369 (tt0) REVERT: C 445 GLU cc_start: 0.6283 (mp0) cc_final: 0.5928 (mp0) REVERT: C 457 GLU cc_start: 0.5830 (mt-10) cc_final: 0.5515 (tm-30) REVERT: C 466 MET cc_start: 0.4150 (ttm) cc_final: 0.3451 (mmp) REVERT: C 526 SER cc_start: 0.6402 (m) cc_final: 0.5944 (p) REVERT: C 531 ARG cc_start: 0.4324 (mtt180) cc_final: 0.3967 (mmt180) REVERT: C 593 LEU cc_start: 0.3193 (OUTLIER) cc_final: 0.2800 (mp) REVERT: C 595 ASP cc_start: 0.4410 (OUTLIER) cc_final: 0.4084 (t0) REVERT: C 604 GLU cc_start: 0.5656 (tt0) cc_final: 0.4996 (tm-30) REVERT: C 613 GLU cc_start: 0.6097 (tt0) cc_final: 0.5646 (mm-30) REVERT: C 669 GLU cc_start: 0.5611 (tt0) cc_final: 0.5317 (mp0) REVERT: C 678 ARG cc_start: 0.1830 (ttp80) cc_final: 0.1067 (ttt180) REVERT: C 710 MET cc_start: 0.4134 (tmm) cc_final: 0.2508 (mpp) REVERT: D 22 ARG cc_start: 0.6278 (OUTLIER) cc_final: 0.5404 (ttt180) REVERT: D 34 GLU cc_start: 0.6557 (pt0) cc_final: 0.5740 (pp20) REVERT: D 105 GLU cc_start: 0.6544 (mt-10) cc_final: 0.6167 (mp0) REVERT: D 108 GLN cc_start: 0.6501 (mt0) cc_final: 0.6120 (mm110) REVERT: D 133 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6007 (mt-10) REVERT: D 142 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6521 (mm-30) REVERT: D 170 ARG cc_start: 0.5724 (ptt180) cc_final: 0.5248 (ptm160) REVERT: D 204 ASP cc_start: 0.5655 (OUTLIER) cc_final: 0.5039 (p0) REVERT: E 26 LYS cc_start: 0.5934 (mttt) cc_final: 0.4990 (tmtt) REVERT: E 65 ILE cc_start: 0.6464 (OUTLIER) cc_final: 0.5973 (mt) REVERT: E 74 MET cc_start: 0.3283 (tmm) cc_final: 0.3053 (tmm) REVERT: E 126 ARG cc_start: 0.4903 (mtt-85) cc_final: 0.4044 (tpp-160) REVERT: E 163 ARG cc_start: 0.3506 (ppt170) cc_final: 0.1670 (ttt180) REVERT: F 54 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.6664 (tmmm) REVERT: G 8 LYS cc_start: 0.6235 (OUTLIER) cc_final: 0.5724 (tmtt) REVERT: G 30 ARG cc_start: 0.7241 (mmm-85) cc_final: 0.6566 (ttp-170) REVERT: G 88 ARG cc_start: 0.7636 (mtt-85) cc_final: 0.6893 (ttp-170) REVERT: G 149 ARG cc_start: 0.7122 (mtt90) cc_final: 0.6873 (mtt-85) REVERT: G 152 ASP cc_start: 0.6352 (m-30) cc_final: 0.5923 (t0) REVERT: G 155 LYS cc_start: 0.7435 (ttmm) cc_final: 0.7038 (ttpt) REVERT: H 9 LYS cc_start: 0.4759 (mmtt) cc_final: 0.4369 (pttp) REVERT: H 13 LEU cc_start: 0.5047 (OUTLIER) cc_final: 0.4824 (mm) REVERT: H 60 GLU cc_start: 0.5337 (tt0) cc_final: 0.4856 (mt-10) REVERT: H 70 MET cc_start: 0.4922 (mtt) cc_final: 0.4642 (mtp) REVERT: H 86 GLN cc_start: 0.3724 (mm-40) cc_final: 0.3524 (mp10) REVERT: I 34 ARG cc_start: 0.7175 (ttm170) cc_final: 0.6598 (ttt180) REVERT: I 54 ASP cc_start: 0.7251 (m-30) cc_final: 0.6560 (p0) REVERT: I 55 SER cc_start: 0.5481 (p) cc_final: 0.4961 (m) REVERT: I 110 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.6869 (mt0) REVERT: J 12 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.5661 (ttm110) REVERT: J 66 ASN cc_start: 0.5450 (t0) cc_final: 0.4991 (t0) REVERT: J 68 HIS cc_start: 0.5617 (m-70) cc_final: 0.4719 (p-80) REVERT: J 112 GLU cc_start: 0.5473 (OUTLIER) cc_final: 0.4675 (tt0) REVERT: L 17 GLU cc_start: 0.5654 (mp0) cc_final: 0.4962 (pm20) REVERT: L 32 LYS cc_start: 0.6971 (mmmt) cc_final: 0.6719 (mtpt) REVERT: L 36 THR cc_start: 0.7559 (OUTLIER) cc_final: 0.7273 (p) REVERT: N 35 ARG cc_start: 0.7182 (mtt180) cc_final: 0.6317 (mtp-110) REVERT: O 19 GLU cc_start: 0.6959 (mp0) cc_final: 0.6750 (mm-30) REVERT: Q 3 GLU cc_start: 0.5984 (mm-30) cc_final: 0.5298 (mt-10) REVERT: Q 50 ASP cc_start: 0.8259 (p0) cc_final: 0.7809 (p0) REVERT: R 16 MET cc_start: 0.6664 (tpp) cc_final: 0.5824 (ptt) REVERT: R 52 TYR cc_start: 0.6136 (t80) cc_final: 0.5920 (t80) REVERT: R 73 GLU cc_start: 0.5361 (mt-10) cc_final: 0.4941 (tp30) REVERT: S 29 ARG cc_start: 0.6757 (mtt90) cc_final: 0.6389 (mtm110) REVERT: S 34 GLN cc_start: 0.6480 (tp-100) cc_final: 0.6171 (tt0) REVERT: T 1 MET cc_start: 0.5191 (OUTLIER) cc_final: 0.4603 (ptp) REVERT: T 3 LYS cc_start: 0.6984 (mttt) cc_final: 0.6312 (tptt) REVERT: T 10 ILE cc_start: 0.6781 (mt) cc_final: 0.6201 (mm) REVERT: T 23 ILE cc_start: 0.4562 (OUTLIER) cc_final: 0.4297 (tt) REVERT: T 33 ASN cc_start: 0.5674 (m110) cc_final: 0.5327 (p0) REVERT: T 36 GLU cc_start: 0.5831 (pt0) cc_final: 0.5329 (pm20) REVERT: T 72 VAL cc_start: 0.5852 (t) cc_final: 0.5333 (m) REVERT: T 84 ASP cc_start: 0.4698 (m-30) cc_final: 0.4314 (t0) REVERT: U 41 ARG cc_start: 0.5930 (mtp180) cc_final: 0.5404 (mtt-85) REVERT: U 47 ARG cc_start: 0.6999 (mtp85) cc_final: 0.5921 (mtm-85) REVERT: U 48 ARG cc_start: 0.6655 (mtm110) cc_final: 0.5632 (mtt180) REVERT: V 19 GLU cc_start: 0.5389 (mt-10) cc_final: 0.4772 (mp0) REVERT: K 20 GLN cc_start: 0.6112 (mt0) cc_final: 0.5569 (tt0) REVERT: K 53 ARG cc_start: 0.5727 (mtm-85) cc_final: 0.5377 (ttm110) REVERT: K 57 LYS cc_start: 0.6369 (OUTLIER) cc_final: 0.5221 (tmtm) outliers start: 95 outliers final: 71 residues processed: 394 average time/residue: 0.6808 time to fit residues: 434.0255 Evaluate side-chains 397 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 307 time to evaluate : 3.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 110 GLN Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 40 HIS Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 244 optimal weight: 4.9990 chunk 393 optimal weight: 5.9990 chunk 239 optimal weight: 0.7980 chunk 186 optimal weight: 10.0000 chunk 273 optimal weight: 4.9990 chunk 412 optimal weight: 4.9990 chunk 379 optimal weight: 0.3980 chunk 328 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 253 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 464 HIS D 123 ASN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 HIS J 5 GLN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 70 ASN ** V 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 55743 Z= 0.216 Angle : 0.617 9.282 81872 Z= 0.320 Chirality : 0.039 0.310 10277 Planarity : 0.005 0.046 5424 Dihedral : 23.744 179.152 24202 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.09 % Favored : 95.77 % Rotamer: Outliers : 3.95 % Allowed : 20.30 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 2884 helix: 0.90 (0.15), residues: 1180 sheet: -0.51 (0.22), residues: 512 loop : -0.97 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 200 HIS 0.013 0.001 HIS V 40 PHE 0.026 0.002 PHE E 31 TYR 0.026 0.002 TYR K 58 ARG 0.007 0.000 ARG H 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 305 time to evaluate : 3.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 LYS cc_start: 0.3473 (mmtt) cc_final: 0.3052 (ttpt) REVERT: C 101 ASN cc_start: 0.2528 (OUTLIER) cc_final: 0.1588 (t0) REVERT: C 103 LEU cc_start: 0.3617 (OUTLIER) cc_final: 0.3115 (pp) REVERT: C 113 MET cc_start: 0.3913 (pmm) cc_final: 0.3352 (pmm) REVERT: C 131 ARG cc_start: 0.5627 (ttt180) cc_final: 0.3454 (tpt90) REVERT: C 218 LYS cc_start: 0.5837 (tttt) cc_final: 0.5091 (tptt) REVERT: C 230 MET cc_start: 0.3033 (mmm) cc_final: 0.2628 (mtp) REVERT: C 266 ASP cc_start: 0.1689 (OUTLIER) cc_final: -0.1099 (p0) REVERT: C 277 ASP cc_start: 0.4608 (m-30) cc_final: 0.4090 (t0) REVERT: C 346 THR cc_start: 0.5610 (m) cc_final: 0.5312 (p) REVERT: C 399 MET cc_start: 0.4152 (ptt) cc_final: 0.3696 (ptp) REVERT: C 430 GLU cc_start: 0.3737 (mp0) cc_final: 0.3176 (tt0) REVERT: C 445 GLU cc_start: 0.6327 (mp0) cc_final: 0.5993 (mp0) REVERT: C 457 GLU cc_start: 0.5862 (mt-10) cc_final: 0.5515 (tm-30) REVERT: C 466 MET cc_start: 0.3931 (ttm) cc_final: 0.3413 (mmp) REVERT: C 526 SER cc_start: 0.6409 (m) cc_final: 0.5945 (p) REVERT: C 593 LEU cc_start: 0.3230 (OUTLIER) cc_final: 0.2794 (mp) REVERT: C 595 ASP cc_start: 0.4441 (OUTLIER) cc_final: 0.4109 (t0) REVERT: C 604 GLU cc_start: 0.5739 (tt0) cc_final: 0.5080 (tm-30) REVERT: C 613 GLU cc_start: 0.6095 (tt0) cc_final: 0.5649 (mm-30) REVERT: C 669 GLU cc_start: 0.5595 (tt0) cc_final: 0.5304 (mp0) REVERT: C 678 ARG cc_start: 0.1792 (ttp80) cc_final: 0.1059 (ttt180) REVERT: C 710 MET cc_start: 0.4012 (tmm) cc_final: 0.2444 (mpp) REVERT: D 22 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.5432 (ttt180) REVERT: D 34 GLU cc_start: 0.6458 (pt0) cc_final: 0.5652 (pp20) REVERT: D 105 GLU cc_start: 0.6546 (mt-10) cc_final: 0.6169 (mp0) REVERT: D 108 GLN cc_start: 0.6491 (mt0) cc_final: 0.6107 (mm110) REVERT: D 133 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.5951 (mp0) REVERT: D 142 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6527 (mm-30) REVERT: D 170 ARG cc_start: 0.5799 (ptt180) cc_final: 0.5319 (ptm160) REVERT: D 204 ASP cc_start: 0.5666 (OUTLIER) cc_final: 0.5052 (p0) REVERT: E 26 LYS cc_start: 0.5894 (mttt) cc_final: 0.4958 (tmtt) REVERT: E 65 ILE cc_start: 0.6471 (OUTLIER) cc_final: 0.5984 (mt) REVERT: E 74 MET cc_start: 0.3165 (tmm) cc_final: 0.2915 (tmm) REVERT: E 126 ARG cc_start: 0.4902 (mtt-85) cc_final: 0.4063 (tpp-160) REVERT: E 163 ARG cc_start: 0.3523 (OUTLIER) cc_final: 0.1662 (ttt180) REVERT: E 187 GLU cc_start: 0.5190 (mt-10) cc_final: 0.4835 (pt0) REVERT: F 54 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.6730 (tmmm) REVERT: G 8 LYS cc_start: 0.6205 (OUTLIER) cc_final: 0.5695 (tmtt) REVERT: G 30 ARG cc_start: 0.7223 (mmm-85) cc_final: 0.6458 (tmm160) REVERT: G 88 ARG cc_start: 0.7646 (mtt-85) cc_final: 0.6782 (ttp-170) REVERT: G 155 LYS cc_start: 0.7434 (ttmm) cc_final: 0.7044 (ttpt) REVERT: H 9 LYS cc_start: 0.4789 (mmtt) cc_final: 0.4394 (pttp) REVERT: H 13 LEU cc_start: 0.5011 (OUTLIER) cc_final: 0.4793 (mm) REVERT: H 60 GLU cc_start: 0.5350 (tt0) cc_final: 0.4863 (mt-10) REVERT: H 70 MET cc_start: 0.4809 (mtt) cc_final: 0.4380 (mtp) REVERT: H 138 ARG cc_start: 0.3707 (tmm160) cc_final: 0.3201 (tmm160) REVERT: I 34 ARG cc_start: 0.7172 (ttm170) cc_final: 0.6599 (ttt180) REVERT: I 54 ASP cc_start: 0.7233 (m-30) cc_final: 0.6590 (p0) REVERT: I 55 SER cc_start: 0.5575 (p) cc_final: 0.5044 (m) REVERT: I 110 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.6876 (mt0) REVERT: J 12 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.5716 (ttm110) REVERT: J 66 ASN cc_start: 0.5388 (t0) cc_final: 0.4964 (t0) REVERT: J 68 HIS cc_start: 0.5625 (m-70) cc_final: 0.4730 (p-80) REVERT: J 112 GLU cc_start: 0.5443 (OUTLIER) cc_final: 0.4665 (tt0) REVERT: L 17 GLU cc_start: 0.5683 (mp0) cc_final: 0.5053 (pm20) REVERT: L 32 LYS cc_start: 0.6972 (mmmt) cc_final: 0.6729 (mtpt) REVERT: L 36 THR cc_start: 0.7581 (OUTLIER) cc_final: 0.7302 (p) REVERT: M 17 ILE cc_start: 0.4040 (mp) cc_final: 0.3783 (mt) REVERT: N 35 ARG cc_start: 0.7146 (mtt180) cc_final: 0.6346 (mtp-110) REVERT: O 19 GLU cc_start: 0.6982 (mp0) cc_final: 0.6745 (mm-30) REVERT: Q 3 GLU cc_start: 0.5977 (mm-30) cc_final: 0.5291 (mt-10) REVERT: Q 50 ASP cc_start: 0.8308 (p0) cc_final: 0.8060 (p0) REVERT: R 16 MET cc_start: 0.6665 (tpp) cc_final: 0.5814 (ptt) REVERT: R 52 TYR cc_start: 0.6122 (t80) cc_final: 0.5867 (t80) REVERT: R 73 GLU cc_start: 0.5329 (mt-10) cc_final: 0.4911 (tp30) REVERT: S 29 ARG cc_start: 0.6756 (mtt90) cc_final: 0.6428 (mtm110) REVERT: S 34 GLN cc_start: 0.6549 (tp-100) cc_final: 0.6241 (tt0) REVERT: T 1 MET cc_start: 0.5179 (OUTLIER) cc_final: 0.4564 (ptp) REVERT: T 3 LYS cc_start: 0.6963 (mttt) cc_final: 0.6310 (tptt) REVERT: T 10 ILE cc_start: 0.6784 (mt) cc_final: 0.6215 (mm) REVERT: T 23 ILE cc_start: 0.4607 (OUTLIER) cc_final: 0.4330 (tt) REVERT: T 33 ASN cc_start: 0.5688 (m110) cc_final: 0.5368 (p0) REVERT: T 36 GLU cc_start: 0.5826 (pt0) cc_final: 0.5339 (pm20) REVERT: T 72 VAL cc_start: 0.5846 (t) cc_final: 0.5338 (m) REVERT: T 84 ASP cc_start: 0.4681 (m-30) cc_final: 0.4324 (t0) REVERT: U 41 ARG cc_start: 0.5914 (mtp180) cc_final: 0.5394 (mtt-85) REVERT: U 47 ARG cc_start: 0.7023 (mtp85) cc_final: 0.5937 (mtm-85) REVERT: U 48 ARG cc_start: 0.6655 (mtm110) cc_final: 0.5633 (mtt180) REVERT: V 19 GLU cc_start: 0.5400 (mt-10) cc_final: 0.4761 (mp0) REVERT: K 20 GLN cc_start: 0.6134 (mt0) cc_final: 0.5594 (tt0) REVERT: K 53 ARG cc_start: 0.5701 (mtm-85) cc_final: 0.5325 (ttm110) REVERT: K 57 LYS cc_start: 0.6391 (OUTLIER) cc_final: 0.5406 (tmtm) outliers start: 99 outliers final: 74 residues processed: 380 average time/residue: 0.6667 time to fit residues: 411.7874 Evaluate side-chains 394 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 300 time to evaluate : 3.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 602 SER Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain G residue 8 LYS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 110 GLN Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain U residue 20 SER Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 260 optimal weight: 0.9980 chunk 349 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 302 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 328 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 337 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 464 HIS E 99 HIS J 5 GLN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 ASN ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 70 ASN ** V 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.125897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.119912 restraints weight = 108310.847| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 0.55 r_work: 0.3826 rms_B_bonded: 0.87 restraints_weight: 0.5000 r_work: 0.3794 rms_B_bonded: 1.78 restraints_weight: 0.2500 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 55743 Z= 0.369 Angle : 0.777 10.140 81872 Z= 0.395 Chirality : 0.046 0.359 10277 Planarity : 0.006 0.049 5424 Dihedral : 23.992 178.734 24202 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.17 % Favored : 94.69 % Rotamer: Outliers : 4.51 % Allowed : 20.10 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 2884 helix: 0.40 (0.15), residues: 1185 sheet: -0.62 (0.22), residues: 488 loop : -1.27 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP E 200 HIS 0.009 0.002 HIS C 569 PHE 0.033 0.003 PHE E 31 TYR 0.021 0.003 TYR K 58 ARG 0.008 0.001 ARG J 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12395.32 seconds wall clock time: 224 minutes 41.16 seconds (13481.16 seconds total)