Starting phenix.real_space_refine on Mon Mar 25 23:07:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cee_16607/03_2024/8cee_16607.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cee_16607/03_2024/8cee_16607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cee_16607/03_2024/8cee_16607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cee_16607/03_2024/8cee_16607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cee_16607/03_2024/8cee_16607.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cee_16607/03_2024/8cee_16607.pdb" } resolution = 3.7 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= 0.000 sd= 0.002 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 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 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 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 "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 173": "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 84": "OE1" <-> "OE2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "I GLU 23": "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 "L GLU 75": "OE1" <-> "OE2" Residue "O GLU 6": "OE1" <-> "OE2" Residue "O GLU 14": "OE1" <-> "OE2" Residue "O GLU 26": "OE1" <-> "OE2" 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 "S GLU 36": "OE1" <-> "OE2" Residue "S ARG 78": "NH1" <-> "NH2" 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 "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 "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 "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 "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 "K GLU 27": "OE1" <-> "OE2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K GLU 66": "OE1" <-> "OE2" Residue "K GLU 99": "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 "R GLU 24": "OE1" <-> "OE2" Residue "R GLU 73": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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': 85, 'rna3p_pur': 643, 'rna3p_pyr': 492} Link IDs: {'rna2p': 197, 'rna3p': 1135} 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: "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: "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: "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: "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: {'PTRANS': 5, '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: "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: "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: "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: "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: "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} 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: "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} Time building chain proxies: 27.88, per 1000 atoms: 0.54 Number of scatterers: 51964 At special positions: 0 Unit cell: (191.2, 226.4, 204, 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=2.04 Simple disulfide: pdb=" SG CYS N 27 " - pdb=" SG CYS N 43 " distance=2.05 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: 29.53 Conformation dependent library (CDL) restraints added in 4.7 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: 98 helices and 33 sheets defined 43.1% alpha, 22.3% beta 425 base pairs and 778 stacking pairs defined. Time for finding SS restraints: 24.45 Creating SS restraints... Processing helix chain 'C' and resid 3 through 15 Processing helix chain 'C' and resid 23 through 31 Processing helix chain 'C' and resid 35 through 52 Processing helix chain 'C' and resid 99 through 103 removed outlier: 3.669A pdb=" N LEU C 103 " --> pdb=" O PRO C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 removed outlier: 3.731A pdb=" N LYS C 171 " --> pdb=" O LYS C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 219 removed outlier: 3.522A pdb=" N VAL C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) 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: 4.078A 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 328 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 removed outlier: 3.591A pdb=" N ALA C 455 " --> pdb=" O PHE C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 493 removed outlier: 4.036A pdb=" N PHE C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 504 removed outlier: 4.179A pdb=" N ILE C 504 " --> pdb=" O ALA C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 516 removed outlier: 3.798A pdb=" N LEU C 509 " --> pdb=" O HIS C 505 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE C 512 " --> pdb=" O ALA C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 531 Processing helix chain 'C' and resid 562 through 576 Processing helix chain 'C' and resid 582 through 624 Proline residue: C 594 - end of helix Processing helix chain 'C' and resid 625 through 627 No H-bonds generated for 'chain 'C' and resid 625 through 627' Processing helix chain 'C' and resid 658 through 660 No H-bonds generated for 'chain 'C' and resid 658 through 660' Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.918A pdb=" N ARG D 29 " --> pdb=" O LYS D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 63 removed outlier: 3.659A pdb=" N LYS D 48 " --> pdb=" O GLN D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 88 removed outlier: 4.785A pdb=" N ASP D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N SER D 79 " --> pdb=" O GLN D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.638A pdb=" N ARG D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 131 through 149 removed outlier: 3.662A pdb=" N VAL D 135 " --> pdb=" O LYS D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 169 through 179 Processing helix chain 'D' and resid 192 through 196 removed outlier: 3.682A pdb=" N GLU D 195 " --> pdb=" O ASP D 192 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE D 196 " --> pdb=" O PRO D 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 192 through 196' Processing helix chain 'D' and resid 206 through 226 Processing helix chain 'F' and resid 7 through 16 removed outlier: 4.153A pdb=" N LEU F 11 " --> pdb=" O PRO F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 62 Processing helix chain 'F' and resid 64 through 78 removed outlier: 3.559A pdb=" N LYS F 77 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU F 78 " --> pdb=" O LYS F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 92 Processing helix chain 'F' and resid 93 through 101 Processing helix chain 'F' and resid 106 through 117 Processing helix chain 'F' and resid 148 through 154 Processing helix chain 'F' and resid 190 through 200 removed outlier: 3.621A pdb=" N ILE F 194 " --> pdb=" O ASN F 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 70 Processing helix chain 'G' and resid 108 through 119 Processing helix chain 'G' and resid 132 through 147 Processing helix chain 'G' and resid 149 through 158 removed outlier: 3.623A pdb=" N ALA G 154 " --> pdb=" O ALA G 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 20 removed outlier: 3.555A pdb=" N VAL I 20 " --> pdb=" O ASN I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 43 Processing helix chain 'I' and resid 97 through 101 Processing helix chain 'I' and resid 115 through 121 Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 21 through 25 removed outlier: 3.629A pdb=" N ASN L 25 " --> pdb=" O SER L 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 21 through 25' Processing helix chain 'L' and resid 127 through 131 Processing helix chain 'O' and resid 5 through 16 Processing helix chain 'O' and resid 24 through 46 removed outlier: 3.639A pdb=" N THR O 45 " --> pdb=" O GLU O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'P' and resid 52 through 63 Processing helix chain 'P' and resid 67 through 78 Processing helix chain 'P' and resid 78 through 88 removed outlier: 3.574A pdb=" N GLN P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 41 removed outlier: 3.708A pdb=" N ILE S 24 " --> pdb=" O HIS S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 64 removed outlier: 3.525A pdb=" N THR S 52 " --> pdb=" O LYS S 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 68 through 85 Processing helix chain 'T' and resid 15 through 33 Processing helix chain 'T' and resid 68 through 82 Processing helix chain 'U' and resid 16 through 21 Processing helix chain 'U' and resid 30 through 36 removed outlier: 3.561A 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 50 through 53 Processing helix chain 'V' and resid 61 through 79 removed outlier: 3.623A pdb=" N HIS V 79 " --> pdb=" O GLY V 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 93 through 105 removed outlier: 4.674A pdb=" N ALA V 97 " --> pdb=" O SER V 93 " (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: 3.530A pdb=" N GLY E 95 " --> pdb=" O ASN E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 125 removed outlier: 3.532A 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: 3.797A pdb=" N GLN E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 31 Processing helix chain 'H' and resid 35 through 55 removed outlier: 3.597A 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: 3.637A 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 '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: 3.940A pdb=" N GLU J 89 " --> pdb=" O ARG J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 101 removed outlier: 3.708A pdb=" N ALA J 101 " --> pdb=" O THR J 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 33 removed outlier: 3.544A pdb=" N LYS K 24 " --> pdb=" O GLN K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 90 removed outlier: 3.537A pdb=" N MET K 88 " --> pdb=" O VAL K 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 21 removed outlier: 3.739A 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: 3.805A 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 'R' and resid 12 through 25 removed outlier: 3.534A 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 sheet with id=AA1, first strand: chain 'C' and resid 56 through 57 Processing sheet with id=AA2, first strand: chain 'C' and resid 96 through 98 removed outlier: 6.697A pdb=" N ILE C 111 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ARG C 115 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL C 129 " --> pdb=" O ARG C 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 139 through 146 removed outlier: 6.104A pdb=" N PHE C 165 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL C 198 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLU C 195 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL C 181 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ILE C 201 " --> pdb=" O LYS C 179 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LYS C 179 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N HIS C 178 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 249 through 251 removed outlier: 4.428A pdb=" N LYS C 364 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU C 355 " --> pdb=" O THR C 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 257 through 260 removed outlier: 6.033A 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 422 through 427 removed outlier: 4.190A pdb=" N GLU C 422 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 472 through 474 Processing sheet with id=AA9, first strand: chain 'C' and resid 630 through 639 removed outlier: 5.564A pdb=" N ILE C 635 " --> pdb=" O GLU C 646 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLU C 646 " --> pdb=" O ILE C 635 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER C 637 " --> pdb=" O PHE C 644 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU C 652 " --> pdb=" O ILE C 703 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N PHE C 705 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU C 654 " --> pdb=" O PHE C 705 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ILE C 707 " --> pdb=" O LEU C 654 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N HIS C 656 " --> pdb=" O ILE C 707 " (cutoff:3.500A) removed outlier: 12.768A pdb=" N GLY C 709 " --> pdb=" O HIS C 656 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU C 706 " --> pdb=" O VAL C 693 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL C 693 " --> pdb=" O GLU C 706 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL C 708 " --> pdb=" O VAL C 691 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL C 691 " --> pdb=" O VAL C 708 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 665 through 668 Processing sheet with id=AB2, first strand: chain 'D' and resid 16 through 19 removed outlier: 5.796A pdb=" N TYR D 39 " --> pdb=" O GLY D 17 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE D 38 " --> pdb=" O GLU D 34 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU D 34 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 4.577A 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: 6.493A pdb=" N ILE D 67 " --> pdb=" O TYR D 90 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL D 92 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N PHE D 69 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU D 68 " --> pdb=" O PHE D 162 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE D 164 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL D 70 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU D 161 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE D 186 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILE D 163 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE D 183 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ILE D 200 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY D 185 " --> pdb=" O ILE D 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 119 through 121 Processing sheet with id=AB5, first strand: chain 'G' and resid 12 through 25 removed outlier: 5.507A pdb=" N GLU G 13 " --> pdb=" O GLY G 40 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY G 40 " --> pdb=" O GLU G 13 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU G 15 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL G 38 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN G 19 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY G 28 " --> pdb=" O VAL G 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 85 through 89 Processing sheet with id=AB7, first strand: chain 'I' and resid 24 through 28 removed outlier: 6.216A pdb=" N ILE I 59 " --> pdb=" O PHE I 51 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE I 51 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG I 61 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL I 49 " --> pdb=" O ARG I 61 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE I 63 " --> pdb=" O ARG I 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 66 through 67 Processing sheet with id=AB9, first strand: chain 'I' and resid 76 through 79 Processing sheet with id=AC1, first strand: chain 'I' and resid 76 through 79 removed outlier: 5.188A pdb=" N VAL I 127 " --> pdb=" O SER I 107 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER I 107 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA I 129 " --> pdb=" O ILE I 105 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 26 through 29 Processing sheet with id=AC3, first strand: chain 'L' and resid 43 through 53 removed outlier: 5.534A pdb=" N CYS L 47 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG L 69 " --> pdb=" O CYS L 47 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG L 49 " --> pdb=" O ARG L 67 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR L 108 " --> pdb=" O THR L 77 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS L 109 " --> pdb=" O ARG L 96 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEU L 94 " --> pdb=" O VAL L 111 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N GLY L 113 " --> pdb=" O VAL L 92 " (cutoff:3.500A) removed outlier: 12.232A pdb=" N VAL L 92 " --> pdb=" O GLY L 113 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 48 through 51 removed outlier: 5.496A pdb=" N THR P 36 " --> pdb=" O VAL P 22 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL P 22 " --> pdb=" O THR P 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Q' and resid 9 through 13 removed outlier: 9.471A pdb=" N PHE Q 75 " --> pdb=" O LYS Q 45 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LYS Q 47 " --> pdb=" O PHE Q 75 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU Q 77 " --> pdb=" O LYS Q 47 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N HIS Q 49 " --> pdb=" O LEU Q 77 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE Q 46 " --> pdb=" O VAL Q 25 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET Q 19 " --> pdb=" O THR Q 22 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR Q 24 " --> pdb=" O ASP Q 17 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ASP Q 17 " --> pdb=" O THR Q 24 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'T' and resid 39 through 52 removed outlier: 5.403A pdb=" N THR T 40 " --> pdb=" O ASN T 64 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ASN T 64 " --> pdb=" O THR T 40 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASP T 42 " --> pdb=" O ILE T 62 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE T 62 " --> pdb=" O ASP T 42 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY T 44 " --> pdb=" O TYR T 60 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR T 60 " --> pdb=" O GLY T 44 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG T 56 " --> pdb=" O LEU T 48 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR T 4 " --> pdb=" O VAL T 65 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG T 87 " --> pdb=" O ILE T 9 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'V' and resid 43 through 48 removed outlier: 7.964A pdb=" N LEU V 84 " --> pdb=" O THR V 110 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE V 112 " --> pdb=" O LEU V 84 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL V 86 " --> pdb=" O ILE V 112 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ASP V 114 " --> pdb=" O VAL V 86 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL V 88 " --> pdb=" O ASP V 114 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 20 through 21 removed outlier: 7.666A pdb=" N LYS E 21 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE E 56 " --> pdb=" O LYS E 21 " (cutoff:3.500A) removed outlier: 4.172A 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=AC9, first strand: chain 'E' and resid 147 through 152 removed outlier: 3.902A pdb=" N THR E 150 " --> pdb=" O TYR E 167 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 179 through 189 removed outlier: 6.013A pdb=" N ASP E 180 " --> pdb=" O ARG E 203 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 73 through 78 Processing sheet with id=AD3, first strand: chain 'J' and resid 6 through 12 Processing sheet with id=AD4, first strand: chain 'K' and resid 35 through 55 removed outlier: 5.029A pdb=" N VAL K 36 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL K 77 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLY K 38 " --> pdb=" O ASP K 75 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ASP K 75 " --> pdb=" O GLY K 38 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS K 71 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N THR K 44 " --> pdb=" O THR K 69 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N THR K 69 " --> pdb=" O THR K 44 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS K 46 " --> pdb=" O MET K 67 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N MET K 67 " --> pdb=" O LYS K 46 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL K 48 " --> pdb=" O PHE K 65 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE K 65 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR K 50 " --> pdb=" O GLU K 63 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLU K 63 " --> pdb=" O THR K 50 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU K 52 " --> pdb=" O SER K 61 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER K 61 " --> pdb=" O LEU K 52 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA K 54 " --> pdb=" O LYS K 59 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LYS K 59 " --> pdb=" O ALA K 54 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS K 11 " --> pdb=" O ASP K 97 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 35 through 55 removed outlier: 5.029A pdb=" N VAL K 36 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL K 77 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLY K 38 " --> pdb=" O ASP K 75 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ASP K 75 " --> pdb=" O GLY K 38 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS K 71 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N THR K 44 " --> pdb=" O THR K 69 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N THR K 69 " --> pdb=" O THR K 44 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS K 46 " --> pdb=" O MET K 67 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N MET K 67 " --> pdb=" O LYS K 46 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL K 48 " --> pdb=" O PHE K 65 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE K 65 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR K 50 " --> pdb=" O GLU K 63 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLU K 63 " --> pdb=" O THR K 50 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU K 52 " --> pdb=" O SER K 61 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER K 61 " --> pdb=" O LEU K 52 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA K 54 " --> pdb=" O LYS K 59 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LYS K 59 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 31 through 33 removed outlier: 6.302A pdb=" N VAL R 31 " --> pdb=" O ALA R 50 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N TYR R 52 " --> pdb=" O VAL R 31 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N THR R 33 " --> pdb=" O TYR R 52 " (cutoff:3.500A) 1137 hydrogen bonds defined for protein. 3249 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1055 hydrogen bonds 1674 hydrogen bond angles 0 basepair planarities 425 basepair parallelities 778 stacking parallelities Total time for adding SS restraints: 40.54 Time building geometry restraints manager: 30.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9124 1.34 - 1.47: 24412 1.47 - 1.60: 19652 1.60 - 1.73: 2422 1.73 - 1.86: 133 Bond restraints: 55743 Sorted by residual: bond pdb=" CA SER P 15 " pdb=" CB SER P 15 " ideal model delta sigma weight residual 1.526 1.468 0.058 1.09e-02 8.42e+03 2.84e+01 bond pdb=" CA SER S 77 " pdb=" CB SER S 77 " ideal model delta sigma weight residual 1.530 1.446 0.085 1.69e-02 3.50e+03 2.51e+01 bond pdb=" P G A 8 " pdb=" O5' G A 8 " ideal model delta sigma weight residual 1.593 1.664 -0.071 1.50e-02 4.44e+03 2.25e+01 bond pdb=" P A B9002 " pdb=" O5' A B9002 " ideal model delta sigma weight residual 1.593 1.653 -0.060 1.50e-02 4.44e+03 1.58e+01 bond pdb=" N VAL L 111 " pdb=" CA VAL L 111 " ideal model delta sigma weight residual 1.460 1.416 0.044 1.10e-02 8.26e+03 1.57e+01 ... (remaining 55738 not shown) Histogram of bond angle deviations from ideal: 93.48 - 101.90: 2259 101.90 - 110.32: 21821 110.32 - 118.74: 31114 118.74 - 127.16: 23511 127.16 - 135.58: 3167 Bond angle restraints: 81872 Sorted by residual: angle pdb=" CA HIS L 109 " pdb=" CB HIS L 109 " pdb=" CG HIS L 109 " ideal model delta sigma weight residual 113.80 103.82 9.98 1.00e+00 1.00e+00 9.97e+01 angle pdb=" CA THR S 13 " pdb=" CB THR S 13 " pdb=" OG1 THR S 13 " ideal model delta sigma weight residual 109.60 94.92 14.68 1.50e+00 4.44e-01 9.58e+01 angle pdb=" O3' C A 980 " pdb=" C3' C A 980 " pdb=" C2' C A 980 " ideal model delta sigma weight residual 109.50 121.39 -11.89 1.50e+00 4.44e-01 6.28e+01 angle pdb=" CA ASN I 16 " pdb=" CB ASN I 16 " pdb=" CG ASN I 16 " ideal model delta sigma weight residual 112.60 104.85 7.75 1.00e+00 1.00e+00 6.01e+01 angle pdb=" C PRO C 66 " pdb=" CA PRO C 66 " pdb=" CB PRO C 66 " ideal model delta sigma weight residual 111.56 124.19 -12.63 1.65e+00 3.67e-01 5.86e+01 ... (remaining 81867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 31820 35.75 - 71.51: 3183 71.51 - 107.26: 472 107.26 - 143.01: 15 143.01 - 178.76: 26 Dihedral angle restraints: 35516 sinusoidal: 27085 harmonic: 8431 Sorted by residual: dihedral pdb=" CA PRO D 130 " pdb=" C PRO D 130 " pdb=" N LYS D 131 " pdb=" CA LYS D 131 " ideal model delta harmonic sigma weight residual -180.00 -93.00 -87.00 0 5.00e+00 4.00e-02 3.03e+02 dihedral pdb=" CA LYS P 45 " pdb=" C LYS P 45 " pdb=" N PRO P 46 " pdb=" CA PRO P 46 " ideal model delta harmonic sigma weight residual 180.00 105.43 74.57 0 5.00e+00 4.00e-02 2.22e+02 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 65.48 81.52 1 8.00e+00 1.56e-02 1.28e+02 ... (remaining 35513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 7795 0.139 - 0.278: 2428 0.278 - 0.418: 46 0.418 - 0.557: 3 0.557 - 0.696: 5 Chirality restraints: 10277 Sorted by residual: chirality pdb=" CA LEU D 10 " pdb=" N LEU D 10 " pdb=" C LEU D 10 " pdb=" CB LEU D 10 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.21e+01 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 -3.00 -0.59 2.00e-01 2.50e+01 8.57e+00 chirality pdb=" P A A 94 " pdb=" OP1 A A 94 " pdb=" OP2 A A 94 " pdb=" O5' A A 94 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.50e+00 ... (remaining 10274 not shown) Planarity restraints: 5424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 146 " -0.616 9.50e-02 1.11e+02 2.77e-01 4.91e+01 pdb=" NE ARG F 146 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG F 146 " 0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG F 146 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG F 146 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 69 " 0.035 2.00e-02 2.50e+03 6.99e-02 4.89e+01 pdb=" C MET C 69 " -0.121 2.00e-02 2.50e+03 pdb=" O MET C 69 " 0.044 2.00e-02 2.50e+03 pdb=" N ASN C 70 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 47 " -0.555 9.50e-02 1.11e+02 2.50e-01 4.35e+01 pdb=" NE ARG I 47 " 0.047 2.00e-02 2.50e+03 pdb=" CZ ARG I 47 " -0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG I 47 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG I 47 " -0.005 2.00e-02 2.50e+03 ... (remaining 5421 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 102 2.48 - 3.09: 34663 3.09 - 3.69: 103381 3.69 - 4.30: 148113 4.30 - 4.90: 205849 Nonbonded interactions: 492108 Sorted by model distance: nonbonded pdb=" O2' A A 979 " pdb=" O2 C A 980 " model vdw 1.876 2.440 nonbonded pdb=" ND1 HIS G 83 " pdb=" O GLU G 84 " model vdw 2.143 2.520 nonbonded pdb=" O LEU P 73 " pdb=" OG SER P 76 " model vdw 2.153 2.440 nonbonded pdb=" O PRO C 66 " pdb=" N MET C 69 " model vdw 2.196 2.520 nonbonded pdb=" O PRO C 66 " pdb=" N ASN C 70 " model vdw 2.219 2.520 ... (remaining 492103 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 group one per residue 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 14.780 Check model and map are aligned: 0.810 Set scattering table: 0.520 Process input model: 173.460 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.160 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 196.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 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 : 0.009 0.085 55743 Z= 0.569 Angle : 1.546 14.680 81872 Z= 0.986 Chirality : 0.111 0.696 10277 Planarity : 0.018 0.277 5424 Dihedral : 23.566 178.763 30066 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.87 % Allowed : 5.89 % Favored : 93.24 % Rotamer: Outliers : 3.87 % Allowed : 5.50 % Favored : 90.63 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.36 % 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: -3.17 (0.13), residues: 2884 helix: -2.49 (0.12), residues: 1141 sheet: -2.00 (0.20), residues: 514 loop : -1.51 (0.16), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.007 TRP E 200 HIS 0.022 0.004 HIS F 116 PHE 0.055 0.006 PHE I 63 TYR 0.058 0.007 TYR S 75 ARG 0.044 0.004 ARG D 110 *********************** 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 667 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 570 time to evaluate : 3.491 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: symmetry clash REVERT: C 44 LYS cc_start: 0.3772 (mttt) cc_final: 0.3259 (mtpp) REVERT: C 59 ARG cc_start: 0.3589 (mmt180) cc_final: 0.3304 (mtp-110) REVERT: C 65 ILE cc_start: -0.0933 (OUTLIER) cc_final: -0.1252 (mp) REVERT: C 113 MET cc_start: 0.3210 (tpp) cc_final: 0.2780 (ptp) REVERT: C 148 ARG cc_start: 0.4010 (OUTLIER) cc_final: 0.3585 (tmt-80) REVERT: C 248 ARG cc_start: 0.2541 (mtt-85) cc_final: 0.2249 (mtt-85) REVERT: C 345 MET cc_start: 0.5496 (mtm) cc_final: 0.4986 (mpp) REVERT: C 386 LYS cc_start: 0.3286 (mttt) cc_final: 0.2816 (ttpp) REVERT: C 411 MET cc_start: 0.5161 (mmt) cc_final: 0.4653 (tmm) REVERT: C 426 LEU cc_start: 0.5014 (mt) cc_final: 0.4788 (tp) REVERT: C 452 MET cc_start: 0.6221 (mmp) cc_final: 0.5420 (ttm) REVERT: C 478 PRO cc_start: 0.7390 (Cg_exo) cc_final: 0.6993 (Cg_endo) REVERT: C 486 PHE cc_start: 0.4467 (t80) cc_final: 0.4120 (t80) REVERT: C 592 ARG cc_start: 0.3435 (mtp180) cc_final: 0.2886 (mmt180) REVERT: C 599 HIS cc_start: 0.4302 (t70) cc_final: 0.4079 (t70) REVERT: C 630 GLU cc_start: 0.2891 (mt-10) cc_final: 0.2629 (mt-10) REVERT: C 671 HIS cc_start: 0.3985 (m90) cc_final: 0.3321 (m90) REVERT: C 672 PHE cc_start: 0.5508 (m-80) cc_final: 0.5187 (m-80) REVERT: C 705 PHE cc_start: 0.2764 (m-10) cc_final: 0.1898 (m-10) REVERT: C 710 MET cc_start: 0.0868 (mtp) cc_final: 0.0301 (mtt) REVERT: D 125 THR cc_start: 0.2795 (m) cc_final: 0.2553 (p) REVERT: D 168 LYS cc_start: 0.7280 (tttt) cc_final: 0.7026 (mmtm) REVERT: F 14 ARG cc_start: 0.7646 (tpp-160) cc_final: 0.7408 (tpt90) REVERT: F 24 LYS cc_start: 0.6192 (pttm) cc_final: 0.5861 (mmmt) REVERT: F 93 ARG cc_start: 0.8507 (mtp85) cc_final: 0.8267 (mtp180) REVERT: F 138 THR cc_start: 0.6268 (m) cc_final: 0.6061 (p) REVERT: F 178 ARG cc_start: 0.5613 (OUTLIER) cc_final: 0.5287 (ptt90) REVERT: F 181 GLU cc_start: 0.5556 (OUTLIER) cc_final: 0.4213 (tt0) REVERT: G 7 SER cc_start: 0.6668 (m) cc_final: 0.6415 (p) REVERT: G 10 GLU cc_start: 0.5242 (OUTLIER) cc_final: 0.4487 (tp30) REVERT: G 11 LEU cc_start: 0.7621 (mt) cc_final: 0.7244 (mp) REVERT: G 54 GLN cc_start: 0.7022 (mt0) cc_final: 0.6811 (pm20) REVERT: G 112 ARG cc_start: 0.6401 (ttm110) cc_final: 0.6122 (ttm170) REVERT: G 149 ARG cc_start: 0.5575 (ttm-80) cc_final: 0.5329 (ttt-90) REVERT: G 151 GLU cc_start: 0.6155 (OUTLIER) cc_final: 0.5829 (mp0) REVERT: I 18 ASN cc_start: 0.8857 (t0) cc_final: 0.8621 (t0) REVERT: I 24 LYS cc_start: 0.6657 (pttt) cc_final: 0.6258 (ptmt) REVERT: I 31 LYS cc_start: 0.6828 (ttpt) cc_final: 0.6167 (ttpp) REVERT: I 42 ARG cc_start: 0.7625 (ttm110) cc_final: 0.7227 (ttp80) REVERT: I 50 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6447 (tp30) REVERT: I 51 PHE cc_start: 0.7254 (m-10) cc_final: 0.6768 (m-10) REVERT: I 54 ASP cc_start: 0.7448 (t70) cc_final: 0.6993 (t0) REVERT: I 70 ASN cc_start: 0.7251 (OUTLIER) cc_final: 0.6775 (p0) REVERT: I 96 ARG cc_start: 0.6151 (mtt90) cc_final: 0.5527 (mtp180) REVERT: I 119 ARG cc_start: 0.6130 (ttm170) cc_final: 0.5886 (mtm180) REVERT: I 122 GLN cc_start: 0.6508 (mt0) cc_final: 0.5899 (mm-40) REVERT: L 20 LYS cc_start: 0.6022 (OUTLIER) cc_final: 0.5675 (ttpt) REVERT: L 34 GLU cc_start: 0.7181 (pt0) cc_final: 0.6332 (mm-30) REVERT: L 37 ASN cc_start: 0.7595 (m-40) cc_final: 0.7220 (t0) REVERT: L 47 CYS cc_start: 0.7219 (m) cc_final: 0.6544 (t) REVERT: L 48 THR cc_start: 0.6965 (p) cc_final: 0.6373 (p) REVERT: L 50 VAL cc_start: 0.5786 (t) cc_final: 0.5480 (p) REVERT: L 67 ARG cc_start: 0.5103 (tpt170) cc_final: 0.4823 (tpt170) REVERT: L 72 ASN cc_start: 0.8785 (p0) cc_final: 0.8474 (p0) REVERT: L 136 LYS cc_start: 0.4324 (OUTLIER) cc_final: 0.3257 (ttpt) REVERT: O 6 GLU cc_start: 0.6834 (pp20) cc_final: 0.6313 (mm-30) REVERT: O 40 ASN cc_start: 0.7208 (m-40) cc_final: 0.6920 (m110) REVERT: O 71 ARG cc_start: 0.7809 (ttp-110) cc_final: 0.7549 (ttm-80) REVERT: O 80 GLU cc_start: 0.7370 (mt-10) cc_final: 0.6916 (tp30) REVERT: P 50 LYS cc_start: 0.8315 (mtmt) cc_final: 0.8090 (mmtt) REVERT: P 79 ILE cc_start: 0.7458 (mt) cc_final: 0.7214 (mm) REVERT: Q 7 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.6549 (mmm-85) REVERT: Q 59 ASP cc_start: 0.7448 (m-30) cc_final: 0.7245 (m-30) REVERT: Q 67 ARG cc_start: 0.8401 (ptt90) cc_final: 0.8171 (ptt-90) REVERT: Q 83 GLU cc_start: 0.6091 (tm-30) cc_final: 0.5664 (tt0) REVERT: S 6 SER cc_start: 0.7663 (OUTLIER) cc_final: 0.7461 (t) REVERT: S 21 ASN cc_start: 0.7420 (m-40) cc_final: 0.7217 (m-40) REVERT: S 43 GLU cc_start: 0.5991 (mm-30) cc_final: 0.5619 (mt-10) REVERT: T 7 MET cc_start: 0.7643 (ttp) cc_final: 0.7367 (ttp) REVERT: T 27 ASN cc_start: 0.6895 (m-40) cc_final: 0.6589 (t0) REVERT: T 50 TYR cc_start: 0.6694 (p90) cc_final: 0.5061 (p90) REVERT: T 56 ARG cc_start: 0.6843 (mtp180) cc_final: 0.6588 (ptt-90) REVERT: T 64 ASN cc_start: 0.6496 (m-40) cc_final: 0.6208 (m-40) REVERT: T 87 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.6221 (tpp80) REVERT: U 32 ASP cc_start: 0.8499 (m-30) cc_final: 0.8230 (p0) REVERT: U 70 MET cc_start: 0.6584 (mmm) cc_final: 0.6097 (mmm) REVERT: E 12 ILE cc_start: 0.0811 (OUTLIER) cc_final: 0.0408 (tp) REVERT: E 48 ASP cc_start: 0.1794 (OUTLIER) cc_final: 0.1540 (t0) REVERT: E 74 MET cc_start: 0.2308 (tmm) cc_final: 0.2076 (ttt) REVERT: H 9 LYS cc_start: 0.3174 (OUTLIER) cc_final: 0.2605 (tmmt) REVERT: H 75 VAL cc_start: 0.3167 (OUTLIER) cc_final: 0.2638 (m) REVERT: R 56 LYS cc_start: 0.1531 (OUTLIER) cc_final: 0.1077 (mmmt) REVERT: R 81 LYS cc_start: 0.0855 (OUTLIER) cc_final: 0.0094 (ptmm) outliers start: 97 outliers final: 12 residues processed: 648 average time/residue: 0.7317 time to fit residues: 743.2359 Evaluate side-chains 447 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 417 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain D residue 23 TRP Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain I residue 70 ASN Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain L residue 20 LYS Chi-restraints excluded: chain L residue 136 LYS Chi-restraints excluded: chain P residue 24 ASP Chi-restraints excluded: chain Q residue 7 ARG Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 87 ARG Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain H residue 9 LYS Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 54 PRO Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 81 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 349 optimal weight: 4.9990 chunk 313 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 211 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 324 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 241 optimal weight: 0.0570 chunk 375 optimal weight: 7.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN C 217 HIS C 297 ASN C 484 GLN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN F 115 ASN G 135 ASN I 57 GLN I 69 ASN L 5 ASN L 25 ASN O 72 ASN Q 11 GLN Q 52 ASN S 14 ASN ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 42 ASN E 136 GLN H 64 GLN H 86 GLN ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 GLN J 81 HIS K 82 GLN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 ASN ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN R 57 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 55743 Z= 0.311 Angle : 0.844 25.438 81872 Z= 0.439 Chirality : 0.049 0.407 10277 Planarity : 0.006 0.075 5424 Dihedral : 24.297 179.036 24231 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.02 % Favored : 96.64 % Rotamer: Outliers : 3.59 % Allowed : 10.65 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.14 % 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: -1.15 (0.15), residues: 2884 helix: -0.04 (0.14), residues: 1168 sheet: -1.48 (0.20), residues: 553 loop : -0.95 (0.18), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 200 HIS 0.011 0.002 HIS M 91 PHE 0.040 0.003 PHE T 26 TYR 0.025 0.003 TYR U 56 ARG 0.011 0.001 ARG G 20 *********************** 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 538 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 448 time to evaluate : 2.912 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: symmetry clash revert: symmetry clash REVERT: C 7 MET cc_start: 0.5406 (mtm) cc_final: 0.5137 (mmt) REVERT: C 69 MET cc_start: 0.0161 (ptt) cc_final: -0.0170 (mpp) REVERT: C 107 MET cc_start: 0.3738 (OUTLIER) cc_final: 0.3458 (pmm) REVERT: C 412 ASP cc_start: 0.7271 (m-30) cc_final: 0.7035 (m-30) REVERT: C 478 PRO cc_start: 0.6944 (Cg_exo) cc_final: 0.6656 (Cg_endo) REVERT: C 631 PHE cc_start: 0.4075 (m-80) cc_final: 0.3745 (m-80) REVERT: C 710 MET cc_start: 0.0974 (mtp) cc_final: 0.0732 (mtt) REVERT: D 168 LYS cc_start: 0.7085 (tttt) cc_final: 0.6830 (mmtm) REVERT: F 14 ARG cc_start: 0.7769 (tpp-160) cc_final: 0.7426 (tpt-90) REVERT: F 24 LYS cc_start: 0.6469 (pttm) cc_final: 0.6167 (mmmt) REVERT: F 53 GLU cc_start: 0.6509 (tp30) cc_final: 0.6221 (mm-30) REVERT: F 138 THR cc_start: 0.6131 (m) cc_final: 0.5883 (p) REVERT: F 168 ASP cc_start: 0.6219 (t0) cc_final: 0.5756 (p0) REVERT: F 181 GLU cc_start: 0.4955 (OUTLIER) cc_final: 0.3764 (tp30) REVERT: G 7 SER cc_start: 0.6798 (m) cc_final: 0.6552 (p) REVERT: G 10 GLU cc_start: 0.5975 (OUTLIER) cc_final: 0.4696 (tp30) REVERT: G 29 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7157 (ptt-90) REVERT: G 43 ASN cc_start: 0.7781 (m-40) cc_final: 0.7490 (t0) REVERT: G 52 LYS cc_start: 0.4985 (tttm) cc_final: 0.4628 (tmtt) REVERT: G 54 GLN cc_start: 0.6970 (mt0) cc_final: 0.6534 (pm20) REVERT: G 58 GLU cc_start: 0.5884 (OUTLIER) cc_final: 0.5528 (tt0) REVERT: G 116 GLU cc_start: 0.6457 (mt-10) cc_final: 0.6206 (mm-30) REVERT: G 149 ARG cc_start: 0.5614 (ttm-80) cc_final: 0.5260 (mtm180) REVERT: I 18 ASN cc_start: 0.8841 (t0) cc_final: 0.8621 (t0) REVERT: I 23 GLU cc_start: 0.7241 (tt0) cc_final: 0.7041 (tm-30) REVERT: I 24 LYS cc_start: 0.6685 (pttt) cc_final: 0.6200 (ptmm) REVERT: I 31 LYS cc_start: 0.6726 (ttpt) cc_final: 0.6388 (tttp) REVERT: I 43 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6864 (mm-30) REVERT: I 50 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6917 (tp30) REVERT: I 96 ARG cc_start: 0.6103 (mtt90) cc_final: 0.5460 (mtp180) REVERT: I 122 GLN cc_start: 0.6780 (mt0) cc_final: 0.6137 (mm-40) REVERT: L 20 LYS cc_start: 0.5906 (OUTLIER) cc_final: 0.5592 (ttpt) REVERT: L 34 GLU cc_start: 0.7096 (pt0) cc_final: 0.6215 (mm-30) REVERT: L 136 LYS cc_start: 0.4278 (OUTLIER) cc_final: 0.3177 (ttpt) REVERT: O 6 GLU cc_start: 0.6869 (pp20) cc_final: 0.6368 (mm-30) REVERT: O 26 GLU cc_start: 0.7353 (mp0) cc_final: 0.7136 (mp0) REVERT: O 34 ASP cc_start: 0.7379 (t0) cc_final: 0.6909 (m-30) REVERT: O 40 ASN cc_start: 0.7310 (m-40) cc_final: 0.7003 (m110) REVERT: O 58 LYS cc_start: 0.7493 (mtpp) cc_final: 0.7267 (mtpp) REVERT: O 77 ARG cc_start: 0.7575 (mtp85) cc_final: 0.7349 (mtm-85) REVERT: O 80 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7045 (tp30) REVERT: P 50 LYS cc_start: 0.8152 (mtmt) cc_final: 0.7948 (mttt) REVERT: P 77 GLN cc_start: 0.7406 (mm-40) cc_final: 0.7124 (mm-40) REVERT: P 79 ILE cc_start: 0.7451 (mt) cc_final: 0.7246 (mm) REVERT: Q 36 TYR cc_start: 0.8083 (m-80) cc_final: 0.7762 (m-80) REVERT: T 27 ASN cc_start: 0.7083 (m-40) cc_final: 0.6616 (t0) REVERT: T 50 TYR cc_start: 0.6531 (p90) cc_final: 0.5460 (p90) REVERT: T 56 ARG cc_start: 0.6527 (mtp180) cc_final: 0.6270 (ptt-90) REVERT: U 32 ASP cc_start: 0.8563 (m-30) cc_final: 0.8213 (p0) REVERT: U 35 LYS cc_start: 0.7701 (mmtt) cc_final: 0.7461 (mttt) REVERT: U 57 GLN cc_start: 0.7198 (tp40) cc_final: 0.6838 (tp40) REVERT: V 67 MET cc_start: 0.3742 (tpp) cc_final: 0.3264 (ttm) REVERT: E 12 ILE cc_start: 0.0882 (OUTLIER) cc_final: 0.0257 (tp) REVERT: E 48 ASP cc_start: 0.1807 (OUTLIER) cc_final: 0.1370 (t0) REVERT: E 74 MET cc_start: 0.2292 (tmm) cc_final: 0.2044 (ttt) REVERT: H 9 LYS cc_start: 0.3121 (OUTLIER) cc_final: 0.2769 (tmtt) REVERT: K 82 GLN cc_start: -0.0153 (OUTLIER) cc_final: -0.0736 (tt0) REVERT: R 56 LYS cc_start: 0.1546 (OUTLIER) cc_final: 0.1154 (mmmt) REVERT: R 81 LYS cc_start: 0.0502 (OUTLIER) cc_final: -0.0703 (ptmm) outliers start: 90 outliers final: 42 residues processed: 515 average time/residue: 0.7329 time to fit residues: 594.7253 Evaluate side-chains 445 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 390 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain D residue 23 TRP Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain L residue 20 LYS Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 136 LYS Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain T residue 54 ASP Chi-restraints excluded: chain T residue 59 PHE Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain V residue 95 ARG Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain H residue 9 LYS Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 56 HIS Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 81 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 208 optimal weight: 5.9990 chunk 116 optimal weight: 20.0000 chunk 312 optimal weight: 0.7980 chunk 256 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 chunk 376 optimal weight: 10.0000 chunk 406 optimal weight: 5.9990 chunk 335 optimal weight: 10.0000 chunk 373 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 302 optimal weight: 3.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 ASN C 178 HIS ** D 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 ASN ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 72 ASN V 30 ASN E 68 HIS E 125 ASN E 133 GLN K 82 GLN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 HIS R 14 HIS R 29 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 55743 Z= 0.282 Angle : 0.756 17.159 81872 Z= 0.394 Chirality : 0.045 0.342 10277 Planarity : 0.006 0.079 5424 Dihedral : 24.232 179.554 24191 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.85 % Favored : 95.87 % Rotamer: Outliers : 4.83 % Allowed : 12.84 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.14 % 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: -0.77 (0.15), residues: 2884 helix: 0.43 (0.14), residues: 1173 sheet: -1.01 (0.21), residues: 555 loop : -1.12 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP P 59 HIS 0.014 0.002 HIS C 505 PHE 0.028 0.003 PHE C 463 TYR 0.024 0.003 TYR U 56 ARG 0.009 0.001 ARG V 95 *********************** 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 537 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 416 time to evaluate : 3.934 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: C 7 MET cc_start: 0.4643 (mtm) cc_final: 0.4343 (mmt) REVERT: C 11 LEU cc_start: 0.2232 (OUTLIER) cc_final: 0.1393 (tp) REVERT: C 69 MET cc_start: -0.0326 (ptt) cc_final: -0.0735 (mtp) REVERT: C 367 GLU cc_start: 0.3902 (tp30) cc_final: 0.3692 (mt-10) REVERT: C 456 ASN cc_start: 0.6419 (m-40) cc_final: 0.6110 (t0) REVERT: C 533 MET cc_start: 0.5365 (tpt) cc_final: 0.4738 (tpp) REVERT: C 575 TYR cc_start: 0.4807 (m-80) cc_final: 0.4436 (m-10) REVERT: C 662 ASP cc_start: 0.4348 (p0) cc_final: 0.3923 (p0) REVERT: C 710 MET cc_start: 0.1569 (mtp) cc_final: 0.1208 (mtt) REVERT: D 93 ASN cc_start: 0.7131 (p0) cc_final: 0.6808 (p0) REVERT: D 168 LYS cc_start: 0.6787 (tttt) cc_final: 0.6347 (mmtm) REVERT: F 14 ARG cc_start: 0.7763 (tpp-160) cc_final: 0.7449 (mmm-85) REVERT: F 138 THR cc_start: 0.5967 (m) cc_final: 0.5738 (p) REVERT: F 181 GLU cc_start: 0.5047 (OUTLIER) cc_final: 0.4832 (tm-30) REVERT: G 7 SER cc_start: 0.6761 (m) cc_final: 0.6547 (p) REVERT: G 10 GLU cc_start: 0.5985 (OUTLIER) cc_final: 0.4934 (tp30) REVERT: G 43 ASN cc_start: 0.7645 (m-40) cc_final: 0.7330 (t0) REVERT: G 52 LYS cc_start: 0.4812 (tttm) cc_final: 0.4301 (tmtt) REVERT: G 54 GLN cc_start: 0.6952 (mt0) cc_final: 0.6606 (pm20) REVERT: G 58 GLU cc_start: 0.5992 (OUTLIER) cc_final: 0.5738 (tt0) REVERT: G 149 ARG cc_start: 0.5509 (ttm-80) cc_final: 0.5187 (ttp-170) REVERT: I 18 ASN cc_start: 0.8866 (t0) cc_final: 0.8599 (t0) REVERT: I 24 LYS cc_start: 0.6661 (pttt) cc_final: 0.6181 (ptmm) REVERT: I 31 LYS cc_start: 0.6461 (ttpt) cc_final: 0.6182 (tttp) REVERT: I 50 GLU cc_start: 0.7271 (mt-10) cc_final: 0.7006 (tp30) REVERT: I 96 ARG cc_start: 0.6149 (mtt90) cc_final: 0.5485 (mtp180) REVERT: L 20 LYS cc_start: 0.5644 (OUTLIER) cc_final: 0.5329 (ttpt) REVERT: L 34 GLU cc_start: 0.7158 (pt0) cc_final: 0.6239 (mm-30) REVERT: L 136 LYS cc_start: 0.4250 (OUTLIER) cc_final: 0.3152 (ttpt) REVERT: O 6 GLU cc_start: 0.6857 (pp20) cc_final: 0.6542 (mm-30) REVERT: O 33 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8211 (p) REVERT: O 34 ASP cc_start: 0.7292 (t0) cc_final: 0.6738 (m-30) REVERT: O 40 ASN cc_start: 0.7363 (m-40) cc_final: 0.7013 (m110) REVERT: O 58 LYS cc_start: 0.7441 (mtpp) cc_final: 0.7188 (mtpp) REVERT: O 71 ARG cc_start: 0.7636 (ttp-110) cc_final: 0.7104 (ttt-90) REVERT: O 80 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6954 (tp30) REVERT: P 45 LYS cc_start: 0.5978 (OUTLIER) cc_final: 0.5700 (mppt) REVERT: P 79 ILE cc_start: 0.7463 (mt) cc_final: 0.7256 (mm) REVERT: S 15 ASN cc_start: 0.7185 (t0) cc_final: 0.6711 (t0) REVERT: T 27 ASN cc_start: 0.6996 (m-40) cc_final: 0.6599 (t0) REVERT: T 36 GLU cc_start: 0.4817 (OUTLIER) cc_final: 0.4273 (mp0) REVERT: T 56 ARG cc_start: 0.6528 (mtp180) cc_final: 0.6276 (ptt-90) REVERT: T 87 ARG cc_start: 0.7100 (tpp80) cc_final: 0.6031 (mmt90) REVERT: U 25 HIS cc_start: 0.5476 (t70) cc_final: 0.5183 (p-80) REVERT: U 35 LYS cc_start: 0.7666 (mmtt) cc_final: 0.7399 (mttt) REVERT: V 67 MET cc_start: 0.3780 (tpp) cc_final: 0.3346 (ttm) REVERT: E 12 ILE cc_start: 0.0933 (OUTLIER) cc_final: 0.0518 (tp) REVERT: E 35 ASP cc_start: 0.2528 (OUTLIER) cc_final: 0.1447 (m-30) REVERT: E 48 ASP cc_start: 0.2077 (OUTLIER) cc_final: 0.1683 (t0) REVERT: E 74 MET cc_start: 0.2175 (tmm) cc_final: 0.1942 (ttt) REVERT: H 9 LYS cc_start: 0.3335 (OUTLIER) cc_final: 0.2840 (tmtt) REVERT: J 100 ARG cc_start: 0.1661 (OUTLIER) cc_final: 0.0956 (ptm160) REVERT: K 82 GLN cc_start: 0.1788 (OUTLIER) cc_final: 0.1050 (tt0) REVERT: R 56 LYS cc_start: 0.1735 (OUTLIER) cc_final: 0.1417 (mmmt) REVERT: R 81 LYS cc_start: 0.0624 (OUTLIER) cc_final: -0.0710 (ptmm) outliers start: 121 outliers final: 61 residues processed: 502 average time/residue: 0.7031 time to fit residues: 568.7134 Evaluate side-chains 454 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 376 time to evaluate : 3.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 605 ARG Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain D residue 23 TRP Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain L residue 20 LYS Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 136 LYS Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain Q residue 54 GLN Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 54 ASP Chi-restraints excluded: chain T residue 59 PHE Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain U residue 69 GLN Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain H residue 9 LYS Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain K residue 56 HIS Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 81 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 372 optimal weight: 10.0000 chunk 283 optimal weight: 7.9990 chunk 195 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 179 optimal weight: 0.1980 chunk 252 optimal weight: 2.9990 chunk 377 optimal weight: 0.0980 chunk 400 optimal weight: 9.9990 chunk 197 optimal weight: 0.8980 chunk 358 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 ASN C 656 HIS D 15 HIS D 93 ASN ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 GLN S 84 ASN T 33 ASN K 82 GLN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 55743 Z= 0.162 Angle : 0.614 11.894 81872 Z= 0.322 Chirality : 0.039 0.356 10277 Planarity : 0.005 0.110 5424 Dihedral : 24.034 179.371 24186 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.67 % Favored : 97.05 % Rotamer: Outliers : 3.23 % Allowed : 14.48 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.11 % 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: -0.21 (0.15), residues: 2884 helix: 1.12 (0.15), residues: 1172 sheet: -0.86 (0.21), residues: 564 loop : -0.99 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 23 HIS 0.007 0.001 HIS C 178 PHE 0.032 0.002 PHE C 13 TYR 0.025 0.002 TYR I 130 ARG 0.007 0.001 ARG S 17 *********************** 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 497 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 416 time to evaluate : 3.380 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: C 7 MET cc_start: 0.4658 (mtm) cc_final: 0.4434 (mmt) REVERT: C 477 GLU cc_start: 0.4955 (mp0) cc_final: 0.4694 (tt0) REVERT: C 533 MET cc_start: 0.5313 (tpt) cc_final: 0.4445 (tpp) REVERT: C 588 LYS cc_start: 0.3276 (tptt) cc_final: 0.2817 (pttp) REVERT: C 603 MET cc_start: 0.4978 (mmp) cc_final: 0.4609 (mmm) REVERT: C 662 ASP cc_start: 0.4588 (p0) cc_final: 0.4264 (p0) REVERT: C 710 MET cc_start: 0.1483 (mtp) cc_final: 0.1204 (mtt) REVERT: D 168 LYS cc_start: 0.6741 (tttt) cc_final: 0.6374 (mmpt) REVERT: D 169 GLU cc_start: 0.6268 (mm-30) cc_final: 0.5798 (mp0) REVERT: F 14 ARG cc_start: 0.7726 (tpp-160) cc_final: 0.7449 (mmm-85) REVERT: F 138 THR cc_start: 0.5778 (m) cc_final: 0.5572 (p) REVERT: F 181 GLU cc_start: 0.4962 (OUTLIER) cc_final: 0.3946 (tp30) REVERT: G 7 SER cc_start: 0.6569 (m) cc_final: 0.6364 (p) REVERT: G 10 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.5195 (tp30) REVERT: G 43 ASN cc_start: 0.7599 (m-40) cc_final: 0.7238 (t0) REVERT: G 54 GLN cc_start: 0.6937 (mt0) cc_final: 0.6508 (pm20) REVERT: G 58 GLU cc_start: 0.6049 (OUTLIER) cc_final: 0.5784 (tt0) REVERT: G 116 GLU cc_start: 0.6607 (mt-10) cc_final: 0.6078 (mm-30) REVERT: I 31 LYS cc_start: 0.6389 (ttpt) cc_final: 0.6087 (tttp) REVERT: I 50 GLU cc_start: 0.7261 (mt-10) cc_final: 0.7031 (tp30) REVERT: I 59 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7375 (mt) REVERT: I 96 ARG cc_start: 0.6133 (mtt90) cc_final: 0.5555 (mtp180) REVERT: L 20 LYS cc_start: 0.5629 (OUTLIER) cc_final: 0.5252 (ttpt) REVERT: L 34 GLU cc_start: 0.7088 (pt0) cc_final: 0.6207 (mm-30) REVERT: L 136 LYS cc_start: 0.4204 (OUTLIER) cc_final: 0.3128 (ttpt) REVERT: O 33 THR cc_start: 0.8618 (m) cc_final: 0.8336 (p) REVERT: O 34 ASP cc_start: 0.7370 (t0) cc_final: 0.6819 (m-30) REVERT: O 40 ASN cc_start: 0.7278 (m-40) cc_final: 0.6932 (m110) REVERT: O 58 LYS cc_start: 0.7422 (mtpp) cc_final: 0.7210 (mtpp) REVERT: O 71 ARG cc_start: 0.7626 (ttp-110) cc_final: 0.7223 (ttm-80) REVERT: O 80 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6911 (tp30) REVERT: P 45 LYS cc_start: 0.5937 (OUTLIER) cc_final: 0.5604 (mppt) REVERT: P 52 ASP cc_start: 0.7015 (t0) cc_final: 0.6735 (t0) REVERT: Q 9 VAL cc_start: 0.8092 (t) cc_final: 0.7734 (p) REVERT: Q 47 LYS cc_start: 0.7727 (mmtp) cc_final: 0.7478 (mmmm) REVERT: T 27 ASN cc_start: 0.7063 (m-40) cc_final: 0.6616 (t0) REVERT: T 50 TYR cc_start: 0.6505 (p90) cc_final: 0.5884 (p90) REVERT: T 56 ARG cc_start: 0.6561 (mtp180) cc_final: 0.6248 (ptt-90) REVERT: T 60 TYR cc_start: 0.7073 (m-80) cc_final: 0.6730 (m-10) REVERT: T 87 ARG cc_start: 0.7010 (tpp80) cc_final: 0.6451 (mmt90) REVERT: U 25 HIS cc_start: 0.5431 (t70) cc_final: 0.5178 (p-80) REVERT: U 35 LYS cc_start: 0.7639 (mmtt) cc_final: 0.7378 (mttt) REVERT: V 67 MET cc_start: 0.3799 (tpp) cc_final: 0.3388 (ttm) REVERT: V 88 VAL cc_start: 0.3495 (t) cc_final: 0.3167 (m) REVERT: E 48 ASP cc_start: 0.2237 (OUTLIER) cc_final: 0.1829 (t0) REVERT: E 74 MET cc_start: 0.2114 (tmm) cc_final: 0.1856 (ttt) REVERT: H 9 LYS cc_start: 0.3373 (OUTLIER) cc_final: 0.3093 (tmtt) REVERT: J 100 ARG cc_start: 0.1642 (OUTLIER) cc_final: 0.0902 (ptm160) REVERT: K 82 GLN cc_start: -0.0448 (OUTLIER) cc_final: -0.0865 (tt0) REVERT: R 56 LYS cc_start: 0.1727 (OUTLIER) cc_final: 0.1469 (mmmt) REVERT: R 81 LYS cc_start: 0.0532 (OUTLIER) cc_final: -0.0903 (ptmm) outliers start: 81 outliers final: 41 residues processed: 470 average time/residue: 0.6979 time to fit residues: 527.8546 Evaluate side-chains 440 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 386 time to evaluate : 3.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 605 ARG Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 656 HIS Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 TRP Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain L residue 20 LYS Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 136 LYS Chi-restraints excluded: chain P residue 10 MET Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 59 PHE Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain H residue 9 LYS Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 56 HIS Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 81 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 333 optimal weight: 9.9990 chunk 227 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 297 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 341 optimal weight: 8.9990 chunk 276 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 204 optimal weight: 0.7980 chunk 359 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 moved from start: 0.4446 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= 0.194 Angle : 0.636 11.803 81872 Z= 0.330 Chirality : 0.040 0.332 10277 Planarity : 0.005 0.113 5424 Dihedral : 24.010 178.788 24184 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.81 % Favored : 95.98 % Rotamer: Outliers : 3.79 % Allowed : 15.56 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.11 % 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: 1.15 (0.15), residues: 1165 sheet: -0.78 (0.21), residues: 554 loop : -1.10 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 18 HIS 0.038 0.002 HIS C 656 PHE 0.024 0.002 PHE C 463 TYR 0.024 0.002 TYR I 130 ARG 0.006 0.001 ARG I 119 *********************** 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 486 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 391 time to evaluate : 3.275 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: C 7 MET cc_start: 0.4572 (mtm) cc_final: 0.4285 (mmt) REVERT: C 20 LYS cc_start: 0.4004 (mtmt) cc_final: 0.3699 (tppt) REVERT: C 224 GLU cc_start: 0.4353 (mt-10) cc_final: 0.4047 (pm20) REVERT: C 440 GLU cc_start: 0.3565 (mt-10) cc_final: 0.3124 (tp30) REVERT: C 456 ASN cc_start: 0.6261 (m-40) cc_final: 0.5980 (t0) REVERT: C 533 MET cc_start: 0.5345 (tpt) cc_final: 0.4732 (tpp) REVERT: C 588 LYS cc_start: 0.3425 (tptt) cc_final: 0.2817 (pttp) REVERT: D 168 LYS cc_start: 0.6645 (tttt) cc_final: 0.6284 (mmpt) REVERT: D 169 GLU cc_start: 0.6355 (mm-30) cc_final: 0.5808 (mp0) REVERT: F 14 ARG cc_start: 0.7736 (tpp-160) cc_final: 0.7397 (mmm-85) REVERT: F 138 THR cc_start: 0.5676 (m) cc_final: 0.5459 (p) REVERT: F 181 GLU cc_start: 0.4890 (OUTLIER) cc_final: 0.3900 (tp30) REVERT: G 7 SER cc_start: 0.6558 (m) cc_final: 0.6352 (p) REVERT: G 10 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.5181 (tp30) REVERT: G 43 ASN cc_start: 0.7607 (m-40) cc_final: 0.7249 (t0) REVERT: G 54 GLN cc_start: 0.6954 (mt0) cc_final: 0.6684 (pm20) REVERT: G 136 MET cc_start: 0.6875 (mtp) cc_final: 0.6611 (mtp) REVERT: I 31 LYS cc_start: 0.6515 (ttpt) cc_final: 0.6232 (tttp) REVERT: I 50 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6987 (tp30) REVERT: I 59 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7279 (mt) REVERT: I 96 ARG cc_start: 0.6084 (mtt90) cc_final: 0.5556 (mtp180) REVERT: L 20 LYS cc_start: 0.5611 (OUTLIER) cc_final: 0.5217 (ttpt) REVERT: L 34 GLU cc_start: 0.7117 (pt0) cc_final: 0.6222 (mm-30) REVERT: L 136 LYS cc_start: 0.4138 (OUTLIER) cc_final: 0.3112 (ttpt) REVERT: O 33 THR cc_start: 0.8599 (m) cc_final: 0.8278 (p) REVERT: O 34 ASP cc_start: 0.7308 (t0) cc_final: 0.6769 (m-30) REVERT: O 40 ASN cc_start: 0.7349 (m-40) cc_final: 0.7037 (m-40) REVERT: O 58 LYS cc_start: 0.7491 (mtpp) cc_final: 0.7252 (mtpp) REVERT: O 71 ARG cc_start: 0.7626 (ttp-110) cc_final: 0.7086 (ttt-90) REVERT: O 80 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6932 (tp30) REVERT: P 45 LYS cc_start: 0.5871 (OUTLIER) cc_final: 0.5567 (mppt) REVERT: Q 47 LYS cc_start: 0.7763 (mmtp) cc_final: 0.7375 (mmmm) REVERT: T 27 ASN cc_start: 0.7215 (m-40) cc_final: 0.6733 (t0) REVERT: T 50 TYR cc_start: 0.6465 (p90) cc_final: 0.5866 (p90) REVERT: T 56 ARG cc_start: 0.6552 (mtp180) cc_final: 0.6253 (ptt-90) REVERT: T 87 ARG cc_start: 0.6986 (tpp80) cc_final: 0.6605 (mmt90) REVERT: U 25 HIS cc_start: 0.5450 (t70) cc_final: 0.5216 (p-80) REVERT: U 35 LYS cc_start: 0.7632 (mmtt) cc_final: 0.7342 (mttt) REVERT: V 67 MET cc_start: 0.3884 (tpp) cc_final: 0.3478 (ttm) REVERT: E 48 ASP cc_start: 0.2373 (OUTLIER) cc_final: 0.1989 (t0) REVERT: E 74 MET cc_start: 0.2235 (tmm) cc_final: 0.2003 (ttt) REVERT: H 9 LYS cc_start: 0.3506 (OUTLIER) cc_final: 0.3257 (tmtt) REVERT: J 100 ARG cc_start: 0.1681 (OUTLIER) cc_final: 0.0950 (ptm160) REVERT: K 52 LEU cc_start: 0.2231 (OUTLIER) cc_final: 0.1647 (mt) REVERT: K 82 GLN cc_start: -0.0269 (OUTLIER) cc_final: -0.0971 (tt0) REVERT: R 56 LYS cc_start: 0.1737 (OUTLIER) cc_final: 0.1472 (mmmt) REVERT: R 81 LYS cc_start: 0.0619 (OUTLIER) cc_final: -0.0545 (pttt) outliers start: 95 outliers final: 65 residues processed: 455 average time/residue: 0.7103 time to fit residues: 521.4709 Evaluate side-chains 449 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 371 time to evaluate : 3.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 605 ARG Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 TRP Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain L residue 20 LYS Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 136 LYS Chi-restraints excluded: chain P residue 10 MET Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 59 PHE Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain U residue 68 ARG Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain H residue 9 LYS Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 56 HIS Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 81 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 134 optimal weight: 1.9990 chunk 360 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 234 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 400 optimal weight: 10.0000 chunk 332 optimal weight: 9.9990 chunk 185 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 210 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 GLN ** C 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 697 ASN D 93 ASN ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 ASN ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS H 64 GLN H 84 ASN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 55743 Z= 0.360 Angle : 0.883 13.884 81872 Z= 0.448 Chirality : 0.049 0.324 10277 Planarity : 0.007 0.118 5424 Dihedral : 24.450 177.827 24184 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.76 % Favored : 94.00 % Rotamer: Outliers : 5.19 % Allowed : 16.15 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.11 % 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: -1.25 (0.15), residues: 2884 helix: 0.19 (0.15), residues: 1148 sheet: -1.22 (0.21), residues: 534 loop : -1.56 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP E 18 HIS 0.011 0.002 HIS C 656 PHE 0.030 0.003 PHE C 463 TYR 0.032 0.003 TYR I 130 ARG 0.013 0.001 ARG I 119 *********************** 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 528 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 398 time to evaluate : 3.452 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 7 MET cc_start: 0.4123 (mtm) cc_final: 0.3814 (mmt) REVERT: C 11 LEU cc_start: 0.2117 (OUTLIER) cc_final: 0.1318 (tp) REVERT: C 20 LYS cc_start: 0.3952 (mtmt) cc_final: 0.3643 (tppt) REVERT: C 133 LEU cc_start: 0.5084 (OUTLIER) cc_final: 0.4817 (tp) REVERT: C 148 ARG cc_start: 0.3554 (OUTLIER) cc_final: 0.2827 (tpt170) REVERT: C 224 GLU cc_start: 0.4306 (mt-10) cc_final: 0.3977 (pm20) REVERT: C 410 ARG cc_start: 0.5413 (ptm-80) cc_final: 0.4903 (tpp80) REVERT: C 440 GLU cc_start: 0.3690 (mt-10) cc_final: 0.3286 (tp30) REVERT: C 456 ASN cc_start: 0.6110 (m-40) cc_final: 0.5889 (t0) REVERT: C 486 PHE cc_start: 0.4814 (t80) cc_final: 0.4441 (t80) REVERT: C 533 MET cc_start: 0.5276 (tpt) cc_final: 0.4674 (tpp) REVERT: C 537 LYS cc_start: 0.4323 (pttt) cc_final: 0.3930 (mptt) REVERT: C 588 LYS cc_start: 0.3213 (tptt) cc_final: 0.2385 (ptpt) REVERT: C 625 ASP cc_start: 0.3842 (OUTLIER) cc_final: 0.3086 (m-30) REVERT: D 96 TRP cc_start: 0.7459 (t-100) cc_final: 0.7071 (t-100) REVERT: D 168 LYS cc_start: 0.6643 (tttt) cc_final: 0.6198 (mmpt) REVERT: F 14 ARG cc_start: 0.7810 (tpp-160) cc_final: 0.7597 (mmm-85) REVERT: F 53 GLU cc_start: 0.6233 (mm-30) cc_final: 0.5679 (mt-10) REVERT: F 138 THR cc_start: 0.5583 (m) cc_final: 0.5349 (p) REVERT: F 181 GLU cc_start: 0.5122 (OUTLIER) cc_final: 0.3957 (tp30) REVERT: G 7 SER cc_start: 0.6731 (m) cc_final: 0.6498 (p) REVERT: G 10 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.5192 (tp30) REVERT: G 43 ASN cc_start: 0.7781 (m-40) cc_final: 0.7556 (t0) REVERT: G 52 LYS cc_start: 0.4799 (tttm) cc_final: 0.4161 (mtmm) REVERT: G 149 ARG cc_start: 0.5200 (ttm-80) cc_final: 0.4507 (ttp-170) REVERT: I 31 LYS cc_start: 0.6419 (ttpt) cc_final: 0.6161 (tttp) REVERT: I 50 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6907 (tp30) REVERT: I 96 ARG cc_start: 0.6080 (mtt90) cc_final: 0.5497 (mtp180) REVERT: L 20 LYS cc_start: 0.5481 (OUTLIER) cc_final: 0.5140 (ttpt) REVERT: L 34 GLU cc_start: 0.7178 (pt0) cc_final: 0.6244 (mm-30) REVERT: L 136 LYS cc_start: 0.4070 (OUTLIER) cc_final: 0.3114 (ttpt) REVERT: O 34 ASP cc_start: 0.7233 (t0) cc_final: 0.6722 (m-30) REVERT: O 80 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6957 (tp30) REVERT: P 45 LYS cc_start: 0.6000 (OUTLIER) cc_final: 0.5691 (mppt) REVERT: Q 47 LYS cc_start: 0.7993 (mmtp) cc_final: 0.7654 (mmmm) REVERT: S 18 ARG cc_start: 0.7586 (ttt90) cc_final: 0.7385 (ttt90) REVERT: T 36 GLU cc_start: 0.4731 (OUTLIER) cc_final: 0.4130 (mp0) REVERT: T 87 ARG cc_start: 0.6880 (tpp80) cc_final: 0.6219 (mmt90) REVERT: U 25 HIS cc_start: 0.5455 (t70) cc_final: 0.5203 (p90) REVERT: U 35 LYS cc_start: 0.7698 (mmtt) cc_final: 0.7424 (mttt) REVERT: E 35 ASP cc_start: 0.1812 (OUTLIER) cc_final: 0.1052 (m-30) REVERT: E 48 ASP cc_start: 0.2604 (OUTLIER) cc_final: 0.2193 (t0) REVERT: E 163 ARG cc_start: 0.2893 (tpt170) cc_final: 0.2465 (ptm160) REVERT: H 9 LYS cc_start: 0.3668 (OUTLIER) cc_final: 0.3277 (tmmt) REVERT: H 30 MET cc_start: 0.3377 (mmt) cc_final: 0.2452 (tpp) REVERT: K 52 LEU cc_start: 0.1572 (OUTLIER) cc_final: 0.1047 (mt) REVERT: K 82 GLN cc_start: 0.0213 (OUTLIER) cc_final: -0.0413 (tp40) REVERT: M 14 ARG cc_start: 0.3563 (mtm180) cc_final: 0.2392 (mmm-85) REVERT: R 56 LYS cc_start: 0.1525 (OUTLIER) cc_final: 0.1201 (mmmt) outliers start: 130 outliers final: 90 residues processed: 495 average time/residue: 0.6886 time to fit residues: 549.9939 Evaluate side-chains 478 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 372 time to evaluate : 3.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 605 ARG Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 625 ASP Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 20 LYS Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 136 LYS Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain Q residue 54 GLN Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 7 MET Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 38 THR Chi-restraints excluded: chain T residue 54 ASP Chi-restraints excluded: chain T residue 59 PHE Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain T residue 85 ILE Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain H residue 9 LYS Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 56 HIS Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 56 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 386 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 228 optimal weight: 0.8980 chunk 292 optimal weight: 0.9980 chunk 226 optimal weight: 6.9990 chunk 337 optimal weight: 9.9990 chunk 223 optimal weight: 1.9990 chunk 399 optimal weight: 5.9990 chunk 249 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 184 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 46 HIS ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 21 ASN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 14 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 55743 Z= 0.155 Angle : 0.624 12.229 81872 Z= 0.325 Chirality : 0.039 0.311 10277 Planarity : 0.005 0.112 5424 Dihedral : 24.088 179.367 24178 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.12 % Favored : 96.64 % Rotamer: Outliers : 2.99 % Allowed : 19.07 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.11 % 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: 0.91 (0.15), residues: 1159 sheet: -0.96 (0.22), residues: 520 loop : -1.27 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 34 HIS 0.013 0.001 HIS R 14 PHE 0.020 0.002 PHE C 418 TYR 0.027 0.002 TYR I 130 ARG 0.008 0.001 ARG T 56 *********************** 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 476 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 401 time to evaluate : 3.499 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: symmetry clash REVERT: C 7 MET cc_start: 0.4590 (mtm) cc_final: 0.4339 (mmt) REVERT: C 113 MET cc_start: 0.2304 (tpp) cc_final: 0.2066 (ptt) REVERT: C 224 GLU cc_start: 0.4243 (mt-10) cc_final: 0.3950 (pm20) REVERT: C 410 ARG cc_start: 0.5450 (ptm-80) cc_final: 0.4942 (tpp80) REVERT: C 440 GLU cc_start: 0.3711 (mt-10) cc_final: 0.3284 (tp30) REVERT: C 456 ASN cc_start: 0.6084 (m-40) cc_final: 0.5850 (t0) REVERT: C 486 PHE cc_start: 0.4582 (t80) cc_final: 0.4109 (t80) REVERT: C 533 MET cc_start: 0.5287 (tpt) cc_final: 0.4678 (tpp) REVERT: C 537 LYS cc_start: 0.4312 (pttt) cc_final: 0.3892 (mptt) REVERT: C 588 LYS cc_start: 0.3274 (tptt) cc_final: 0.2707 (ptmm) REVERT: C 625 ASP cc_start: 0.3675 (OUTLIER) cc_final: 0.2933 (m-30) REVERT: D 110 ARG cc_start: 0.4952 (mmt90) cc_final: 0.4170 (mtt180) REVERT: D 168 LYS cc_start: 0.6555 (tttt) cc_final: 0.6153 (mmpt) REVERT: F 24 LYS cc_start: 0.6546 (OUTLIER) cc_final: 0.6209 (tptm) REVERT: F 68 PHE cc_start: 0.6986 (t80) cc_final: 0.6445 (t80) REVERT: F 138 THR cc_start: 0.5533 (m) cc_final: 0.5327 (p) REVERT: G 7 SER cc_start: 0.6552 (m) cc_final: 0.6342 (p) REVERT: G 10 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.5265 (tp30) REVERT: G 30 ARG cc_start: 0.7246 (mmm-85) cc_final: 0.6838 (ptt90) REVERT: G 43 ASN cc_start: 0.7752 (m-40) cc_final: 0.7530 (t0) REVERT: G 54 GLN cc_start: 0.6996 (mt0) cc_final: 0.6440 (pm20) REVERT: G 116 GLU cc_start: 0.6457 (mt-10) cc_final: 0.5883 (mm-30) REVERT: I 31 LYS cc_start: 0.6385 (ttpt) cc_final: 0.6096 (tttp) REVERT: I 50 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6923 (tp30) REVERT: L 20 LYS cc_start: 0.5576 (OUTLIER) cc_final: 0.5207 (ttpt) REVERT: L 34 GLU cc_start: 0.7098 (pt0) cc_final: 0.6239 (mm-30) REVERT: L 136 LYS cc_start: 0.4272 (OUTLIER) cc_final: 0.3167 (ttpt) REVERT: O 33 THR cc_start: 0.8612 (m) cc_final: 0.8301 (p) REVERT: O 34 ASP cc_start: 0.7168 (t0) cc_final: 0.6603 (m-30) REVERT: O 40 ASN cc_start: 0.7473 (m-40) cc_final: 0.7160 (m-40) REVERT: O 58 LYS cc_start: 0.7646 (mtpp) cc_final: 0.7370 (mtpp) REVERT: O 80 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6936 (tp30) REVERT: P 45 LYS cc_start: 0.5887 (OUTLIER) cc_final: 0.5571 (mppt) REVERT: Q 47 LYS cc_start: 0.7858 (mmtp) cc_final: 0.7554 (mmmm) REVERT: Q 83 GLU cc_start: 0.6040 (tp30) cc_final: 0.5525 (mp0) REVERT: T 27 ASN cc_start: 0.7269 (m-40) cc_final: 0.6701 (t0) REVERT: T 36 GLU cc_start: 0.4656 (OUTLIER) cc_final: 0.4082 (mp0) REVERT: T 87 ARG cc_start: 0.6954 (tpp80) cc_final: 0.6399 (mmt90) REVERT: U 35 LYS cc_start: 0.7612 (mmtt) cc_final: 0.7333 (mttt) REVERT: V 67 MET cc_start: 0.3773 (tpp) cc_final: 0.3261 (ttm) REVERT: E 74 MET cc_start: 0.2494 (ttt) cc_final: 0.2291 (mtm) REVERT: H 9 LYS cc_start: 0.3503 (OUTLIER) cc_final: 0.3164 (tmtt) REVERT: H 30 MET cc_start: 0.3612 (mmt) cc_final: 0.3157 (pmm) REVERT: K 52 LEU cc_start: 0.1680 (OUTLIER) cc_final: 0.1163 (mt) REVERT: M 14 ARG cc_start: 0.3890 (mtm180) cc_final: 0.2786 (mmm-85) REVERT: R 56 LYS cc_start: 0.1566 (OUTLIER) cc_final: 0.1306 (mmmt) REVERT: R 81 LYS cc_start: 0.0716 (OUTLIER) cc_final: -0.0567 (pttt) outliers start: 75 outliers final: 47 residues processed: 452 average time/residue: 0.7103 time to fit residues: 513.6388 Evaluate side-chains 439 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 381 time to evaluate : 3.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 605 ARG Chi-restraints excluded: chain C residue 625 ASP Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain F residue 24 LYS Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 20 LYS Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 136 LYS Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain S residue 28 MET Chi-restraints excluded: chain T residue 7 MET Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 59 PHE Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain U residue 68 ARG Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain H residue 9 LYS Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 81 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 246 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 238 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 253 optimal weight: 0.3980 chunk 271 optimal weight: 8.9990 chunk 197 optimal weight: 0.3980 chunk 37 optimal weight: 6.9990 chunk 313 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN ** C 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 55743 Z= 0.270 Angle : 0.733 12.006 81872 Z= 0.373 Chirality : 0.043 0.308 10277 Planarity : 0.006 0.123 5424 Dihedral : 24.153 179.442 24175 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.31 % Favored : 94.49 % Rotamer: Outliers : 3.91 % Allowed : 18.83 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.11 % 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: -0.80 (0.15), residues: 2884 helix: 0.66 (0.15), residues: 1155 sheet: -1.05 (0.22), residues: 520 loop : -1.41 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 34 HIS 0.007 0.001 HIS K 56 PHE 0.023 0.002 PHE C 418 TYR 0.022 0.002 TYR J 7 ARG 0.009 0.001 ARG I 119 *********************** 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 487 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 389 time to evaluate : 3.493 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 7 MET cc_start: 0.4324 (mtm) cc_final: 0.4086 (mmt) REVERT: C 11 LEU cc_start: 0.2106 (OUTLIER) cc_final: 0.1572 (tp) REVERT: C 20 LYS cc_start: 0.3994 (mtmt) cc_final: 0.3653 (tppt) REVERT: C 51 GLU cc_start: 0.1652 (mt-10) cc_final: 0.1275 (tt0) REVERT: C 148 ARG cc_start: 0.3409 (OUTLIER) cc_final: 0.2712 (tpt170) REVERT: C 224 GLU cc_start: 0.4290 (mt-10) cc_final: 0.3987 (pm20) REVERT: C 410 ARG cc_start: 0.5344 (ptm-80) cc_final: 0.4874 (tpp80) REVERT: C 440 GLU cc_start: 0.3622 (mt-10) cc_final: 0.3244 (tp30) REVERT: C 452 MET cc_start: 0.6796 (mmm) cc_final: 0.5962 (mtm) REVERT: C 456 ASN cc_start: 0.5994 (m-40) cc_final: 0.5783 (t0) REVERT: C 486 PHE cc_start: 0.4709 (t80) cc_final: 0.4267 (t80) REVERT: C 533 MET cc_start: 0.5233 (tpt) cc_final: 0.4637 (tpp) REVERT: C 537 LYS cc_start: 0.4385 (pttt) cc_final: 0.3976 (mptt) REVERT: C 588 LYS cc_start: 0.3074 (tptt) cc_final: 0.2322 (ptpt) REVERT: C 625 ASP cc_start: 0.3694 (OUTLIER) cc_final: 0.2935 (m-30) REVERT: D 110 ARG cc_start: 0.4841 (mmt90) cc_final: 0.4449 (mtt180) REVERT: D 168 LYS cc_start: 0.6552 (tttt) cc_final: 0.6128 (mmpt) REVERT: F 181 GLU cc_start: 0.5176 (OUTLIER) cc_final: 0.3803 (tp30) REVERT: G 7 SER cc_start: 0.6675 (m) cc_final: 0.6442 (p) REVERT: G 10 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.5238 (tp30) REVERT: I 31 LYS cc_start: 0.6381 (ttpt) cc_final: 0.6110 (tttp) REVERT: I 50 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6924 (tp30) REVERT: I 96 ARG cc_start: 0.6106 (mtt90) cc_final: 0.5535 (mtp180) REVERT: L 20 LYS cc_start: 0.5546 (OUTLIER) cc_final: 0.5184 (ttpt) REVERT: L 34 GLU cc_start: 0.7144 (pt0) cc_final: 0.6235 (mm-30) REVERT: L 136 LYS cc_start: 0.4116 (OUTLIER) cc_final: 0.3134 (ttpt) REVERT: O 34 ASP cc_start: 0.7198 (t0) cc_final: 0.6702 (m-30) REVERT: O 58 LYS cc_start: 0.7665 (mtpp) cc_final: 0.7391 (mtpp) REVERT: O 80 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6968 (tp30) REVERT: P 45 LYS cc_start: 0.5917 (OUTLIER) cc_final: 0.5637 (mppt) REVERT: Q 47 LYS cc_start: 0.7969 (mmtp) cc_final: 0.7655 (mmmm) REVERT: Q 51 GLU cc_start: 0.7367 (tp30) cc_final: 0.6896 (tp30) REVERT: S 18 ARG cc_start: 0.7638 (ttt90) cc_final: 0.7430 (ttt90) REVERT: T 7 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.7156 (ttp) REVERT: T 36 GLU cc_start: 0.4666 (OUTLIER) cc_final: 0.4084 (mp0) REVERT: T 62 ILE cc_start: 0.7174 (mt) cc_final: 0.6615 (pt) REVERT: T 87 ARG cc_start: 0.6923 (tpp80) cc_final: 0.6263 (mmt90) REVERT: U 75 TYR cc_start: 0.4577 (m-80) cc_final: 0.3366 (m-80) REVERT: E 163 ARG cc_start: 0.2759 (tpt170) cc_final: 0.2244 (ptm160) REVERT: H 9 LYS cc_start: 0.3525 (OUTLIER) cc_final: 0.3221 (tmmt) REVERT: H 30 MET cc_start: 0.3586 (mmt) cc_final: 0.2640 (tpp) REVERT: K 52 LEU cc_start: 0.1766 (OUTLIER) cc_final: 0.1238 (mt) REVERT: M 79 ARG cc_start: 0.1438 (ptm160) cc_final: 0.0580 (ptm-80) REVERT: R 56 LYS cc_start: 0.1507 (OUTLIER) cc_final: 0.1239 (mmmt) outliers start: 98 outliers final: 76 residues processed: 455 average time/residue: 0.7140 time to fit residues: 521.6249 Evaluate side-chains 472 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 383 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 605 ARG Chi-restraints excluded: chain C residue 625 ASP Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 20 LYS Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 136 LYS Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain Q residue 19 MET Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain S residue 28 MET Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 7 MET Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 38 THR Chi-restraints excluded: chain T residue 59 PHE Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain U residue 68 ARG Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain H residue 9 LYS Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 56 HIS Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 56 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 362 optimal weight: 8.9990 chunk 382 optimal weight: 0.0770 chunk 348 optimal weight: 0.8980 chunk 371 optimal weight: 0.6980 chunk 223 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 291 optimal weight: 0.9980 chunk 114 optimal weight: 20.0000 chunk 336 optimal weight: 8.9990 chunk 351 optimal weight: 6.9990 chunk 370 optimal weight: 0.6980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 HIS C 360 GLN C 467 ASN C 535 GLN ** C 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 55743 Z= 0.138 Angle : 0.592 11.702 81872 Z= 0.306 Chirality : 0.037 0.268 10277 Planarity : 0.005 0.127 5424 Dihedral : 23.959 179.969 24175 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.09 % Favored : 96.74 % Rotamer: Outliers : 2.59 % Allowed : 20.54 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.11 % 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: -0.28 (0.15), residues: 2884 helix: 1.19 (0.15), residues: 1154 sheet: -0.81 (0.22), residues: 527 loop : -1.22 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 46 HIS 0.003 0.001 HIS F 116 PHE 0.021 0.002 PHE C 165 TYR 0.020 0.001 TYR J 94 ARG 0.006 0.001 ARG S 29 *********************** 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 473 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 408 time to evaluate : 3.227 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: symmetry clash REVERT: C 7 MET cc_start: 0.4696 (mtm) cc_final: 0.4447 (mmt) REVERT: C 14 MET cc_start: 0.2644 (mtt) cc_final: 0.1911 (mtp) REVERT: C 20 LYS cc_start: 0.4043 (mtmt) cc_final: 0.3672 (tppt) REVERT: C 51 GLU cc_start: 0.1484 (mt-10) cc_final: 0.1030 (tt0) REVERT: C 148 ARG cc_start: 0.3423 (OUTLIER) cc_final: 0.2740 (tpt170) REVERT: C 224 GLU cc_start: 0.4186 (mt-10) cc_final: 0.3859 (pm20) REVERT: C 410 ARG cc_start: 0.5395 (ptm-80) cc_final: 0.4960 (tpp80) REVERT: C 440 GLU cc_start: 0.3378 (mt-10) cc_final: 0.2918 (tp30) REVERT: C 452 MET cc_start: 0.6794 (mmm) cc_final: 0.5934 (mtm) REVERT: C 456 ASN cc_start: 0.6072 (m-40) cc_final: 0.5847 (t0) REVERT: C 533 MET cc_start: 0.5231 (tpt) cc_final: 0.4655 (tpp) REVERT: C 588 LYS cc_start: 0.3261 (tptt) cc_final: 0.2652 (ptmm) REVERT: C 625 ASP cc_start: 0.3601 (OUTLIER) cc_final: 0.2783 (m-30) REVERT: D 110 ARG cc_start: 0.4765 (mmt90) cc_final: 0.4321 (mtt90) REVERT: D 167 ARG cc_start: 0.5991 (ttt180) cc_final: 0.5731 (mtp85) REVERT: D 168 LYS cc_start: 0.6507 (tttt) cc_final: 0.6205 (mmpt) REVERT: D 169 GLU cc_start: 0.6342 (mm-30) cc_final: 0.5908 (mp0) REVERT: F 24 LYS cc_start: 0.6589 (pttp) cc_final: 0.6248 (tptm) REVERT: F 53 GLU cc_start: 0.5989 (mm-30) cc_final: 0.5498 (mt-10) REVERT: F 68 PHE cc_start: 0.7009 (t80) cc_final: 0.6466 (t80) REVERT: G 7 SER cc_start: 0.6547 (m) cc_final: 0.6321 (p) REVERT: G 10 GLU cc_start: 0.6464 (OUTLIER) cc_final: 0.5281 (tp30) REVERT: G 30 ARG cc_start: 0.7280 (mmm-85) cc_final: 0.6858 (ptt90) REVERT: G 54 GLN cc_start: 0.7085 (mt0) cc_final: 0.6661 (pm20) REVERT: G 116 GLU cc_start: 0.6541 (mt-10) cc_final: 0.5979 (mm-30) REVERT: G 136 MET cc_start: 0.6865 (mtp) cc_final: 0.6652 (mtp) REVERT: G 149 ARG cc_start: 0.5247 (ttm-80) cc_final: 0.4498 (ttp-170) REVERT: I 50 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6948 (tp30) REVERT: L 20 LYS cc_start: 0.5641 (OUTLIER) cc_final: 0.5248 (ttpt) REVERT: L 34 GLU cc_start: 0.7035 (pt0) cc_final: 0.6191 (mm-30) REVERT: L 56 LYS cc_start: 0.4930 (pttp) cc_final: 0.4657 (ptpt) REVERT: L 136 LYS cc_start: 0.4298 (OUTLIER) cc_final: 0.3224 (ttpt) REVERT: O 33 THR cc_start: 0.8598 (m) cc_final: 0.8293 (p) REVERT: O 34 ASP cc_start: 0.7214 (t0) cc_final: 0.6683 (m-30) REVERT: O 40 ASN cc_start: 0.7422 (m-40) cc_final: 0.7116 (m-40) REVERT: O 58 LYS cc_start: 0.7627 (mtpp) cc_final: 0.7342 (mtpp) REVERT: O 80 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6933 (tp30) REVERT: P 45 LYS cc_start: 0.5712 (OUTLIER) cc_final: 0.5393 (mppt) REVERT: Q 47 LYS cc_start: 0.7850 (mmtp) cc_final: 0.7563 (mmmm) REVERT: Q 51 GLU cc_start: 0.7286 (tp30) cc_final: 0.6866 (tp30) REVERT: Q 83 GLU cc_start: 0.6200 (tp30) cc_final: 0.5634 (mp0) REVERT: T 36 GLU cc_start: 0.4538 (OUTLIER) cc_final: 0.3945 (mp0) REVERT: T 56 ARG cc_start: 0.6713 (mmt180) cc_final: 0.6323 (ptt-90) REVERT: T 87 ARG cc_start: 0.6887 (tpp80) cc_final: 0.6329 (mmt90) REVERT: U 35 LYS cc_start: 0.7420 (mmtt) cc_final: 0.7028 (mttt) REVERT: U 75 TYR cc_start: 0.4541 (m-80) cc_final: 0.3294 (m-80) REVERT: V 67 MET cc_start: 0.3926 (tpp) cc_final: 0.3303 (ttm) REVERT: E 74 MET cc_start: 0.2512 (ttt) cc_final: 0.2293 (mtm) REVERT: H 9 LYS cc_start: 0.3527 (OUTLIER) cc_final: 0.3247 (tmmt) REVERT: H 30 MET cc_start: 0.3743 (mmt) cc_final: 0.3275 (pmm) REVERT: J 100 ARG cc_start: 0.1497 (OUTLIER) cc_final: 0.0717 (ptp-170) REVERT: K 52 LEU cc_start: 0.1834 (OUTLIER) cc_final: 0.1329 (mt) REVERT: M 14 ARG cc_start: 0.4215 (mtm180) cc_final: 0.3054 (mmm-85) REVERT: M 79 ARG cc_start: 0.1479 (ptm160) cc_final: 0.0671 (ptm-80) REVERT: R 56 LYS cc_start: 0.1536 (OUTLIER) cc_final: 0.1237 (tptt) REVERT: R 81 LYS cc_start: 0.0923 (OUTLIER) cc_final: -0.0361 (pttt) outliers start: 65 outliers final: 45 residues processed: 451 average time/residue: 0.6982 time to fit residues: 504.1052 Evaluate side-chains 447 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 390 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 605 ARG Chi-restraints excluded: chain C residue 625 ASP Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 20 LYS Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 136 LYS Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain Q residue 19 MET Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain S residue 28 MET Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 38 THR Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain H residue 9 LYS Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 56 LYS Chi-restraints excluded: chain R residue 81 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 244 optimal weight: 0.9990 chunk 393 optimal weight: 0.9980 chunk 239 optimal weight: 7.9990 chunk 186 optimal weight: 3.9990 chunk 273 optimal weight: 5.9990 chunk 412 optimal weight: 0.9980 chunk 379 optimal weight: 0.9980 chunk 328 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 253 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 ASN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.5789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 55743 Z= 0.147 Angle : 0.583 10.798 81872 Z= 0.300 Chirality : 0.036 0.272 10277 Planarity : 0.005 0.127 5424 Dihedral : 23.861 179.356 24173 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.61 % Favored : 96.22 % Rotamer: Outliers : 2.31 % Allowed : 21.22 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.11 % 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: -0.04 (0.16), residues: 2884 helix: 1.37 (0.15), residues: 1151 sheet: -0.52 (0.23), residues: 512 loop : -1.14 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP T 43 HIS 0.004 0.001 HIS R 14 PHE 0.022 0.002 PHE C 165 TYR 0.017 0.001 TYR F 131 ARG 0.008 0.000 ARG C 531 ********************** 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 446 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 388 time to evaluate : 3.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 7 MET cc_start: 0.4825 (mtm) cc_final: 0.4613 (mmt) REVERT: C 51 GLU cc_start: 0.1522 (mt-10) cc_final: 0.1056 (tt0) REVERT: C 148 ARG cc_start: 0.3583 (OUTLIER) cc_final: 0.2959 (tpt170) REVERT: C 224 GLU cc_start: 0.4305 (mt-10) cc_final: 0.4031 (pm20) REVERT: C 258 THR cc_start: 0.5083 (p) cc_final: 0.4878 (p) REVERT: C 410 ARG cc_start: 0.5460 (ptm-80) cc_final: 0.5024 (tpp80) REVERT: C 440 GLU cc_start: 0.3317 (mt-10) cc_final: 0.2847 (tp30) REVERT: C 452 MET cc_start: 0.6780 (mmm) cc_final: 0.6415 (mpp) REVERT: C 456 ASN cc_start: 0.6077 (m-40) cc_final: 0.5844 (t0) REVERT: C 477 GLU cc_start: 0.4675 (mp0) cc_final: 0.4395 (tt0) REVERT: C 533 MET cc_start: 0.5225 (tpt) cc_final: 0.4658 (tpp) REVERT: C 537 LYS cc_start: 0.4463 (pttt) cc_final: 0.4038 (mptt) REVERT: C 588 LYS cc_start: 0.3203 (tptt) cc_final: 0.2583 (pttp) REVERT: C 603 MET cc_start: 0.4889 (mmp) cc_final: 0.4574 (mmm) REVERT: C 625 ASP cc_start: 0.3561 (OUTLIER) cc_final: 0.2771 (m-30) REVERT: C 705 PHE cc_start: 0.3417 (m-80) cc_final: 0.2655 (m-80) REVERT: D 110 ARG cc_start: 0.4729 (mmt90) cc_final: 0.4460 (mtt90) REVERT: D 167 ARG cc_start: 0.5985 (ttt180) cc_final: 0.5717 (mtp85) REVERT: D 168 LYS cc_start: 0.6512 (tttt) cc_final: 0.6217 (mmpt) REVERT: D 169 GLU cc_start: 0.6367 (mm-30) cc_final: 0.5919 (mp0) REVERT: D 223 GLU cc_start: 0.6153 (mm-30) cc_final: 0.5632 (pt0) REVERT: F 24 LYS cc_start: 0.6657 (pttp) cc_final: 0.6261 (tptm) REVERT: F 53 GLU cc_start: 0.6184 (mm-30) cc_final: 0.5492 (mt-10) REVERT: G 7 SER cc_start: 0.6562 (m) cc_final: 0.6331 (p) REVERT: G 30 ARG cc_start: 0.7308 (mmm-85) cc_final: 0.6869 (ptt90) REVERT: G 54 GLN cc_start: 0.7077 (mt0) cc_final: 0.6699 (pm20) REVERT: G 116 GLU cc_start: 0.6503 (mt-10) cc_final: 0.5971 (mm-30) REVERT: G 136 MET cc_start: 0.6840 (mtp) cc_final: 0.6618 (mtp) REVERT: I 50 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6978 (tp30) REVERT: L 20 LYS cc_start: 0.5664 (OUTLIER) cc_final: 0.5254 (ttpt) REVERT: L 34 GLU cc_start: 0.7060 (pt0) cc_final: 0.6200 (mm-30) REVERT: L 56 LYS cc_start: 0.4944 (pttp) cc_final: 0.4684 (ptpt) REVERT: L 136 LYS cc_start: 0.4227 (OUTLIER) cc_final: 0.3128 (ttpt) REVERT: O 33 THR cc_start: 0.8686 (m) cc_final: 0.8367 (p) REVERT: O 34 ASP cc_start: 0.7220 (t0) cc_final: 0.6682 (m-30) REVERT: O 40 ASN cc_start: 0.7388 (m-40) cc_final: 0.7076 (m-40) REVERT: O 58 LYS cc_start: 0.7693 (mtpp) cc_final: 0.7397 (mtpp) REVERT: O 76 THR cc_start: 0.4900 (OUTLIER) cc_final: 0.4687 (t) REVERT: O 80 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6904 (tp30) REVERT: P 45 LYS cc_start: 0.5629 (OUTLIER) cc_final: 0.5343 (mppt) REVERT: Q 47 LYS cc_start: 0.7816 (mmtp) cc_final: 0.7532 (mmmm) REVERT: Q 83 GLU cc_start: 0.6111 (tp30) cc_final: 0.5635 (mp0) REVERT: S 18 ARG cc_start: 0.7228 (ttt90) cc_final: 0.7006 (tpp80) REVERT: T 36 GLU cc_start: 0.4569 (OUTLIER) cc_final: 0.4134 (mp0) REVERT: T 56 ARG cc_start: 0.6682 (mmt180) cc_final: 0.6311 (ptt-90) REVERT: T 87 ARG cc_start: 0.6921 (tpp80) cc_final: 0.6375 (mmt90) REVERT: U 35 LYS cc_start: 0.7446 (mmtt) cc_final: 0.7055 (mttt) REVERT: U 75 TYR cc_start: 0.4542 (m-80) cc_final: 0.3298 (m-80) REVERT: V 67 MET cc_start: 0.3910 (tpp) cc_final: 0.3283 (ttm) REVERT: H 9 LYS cc_start: 0.3616 (OUTLIER) cc_final: 0.3312 (tmtt) REVERT: H 30 MET cc_start: 0.3753 (mmt) cc_final: 0.2806 (tpp) REVERT: J 100 ARG cc_start: 0.1529 (OUTLIER) cc_final: 0.0770 (ptp-170) REVERT: K 52 LEU cc_start: 0.1934 (OUTLIER) cc_final: 0.1463 (mt) REVERT: M 14 ARG cc_start: 0.4184 (mtm180) cc_final: 0.3076 (mmm-85) REVERT: M 79 ARG cc_start: 0.1342 (ptm160) cc_final: 0.0519 (ptm-80) REVERT: R 56 LYS cc_start: 0.1599 (OUTLIER) cc_final: 0.1282 (tptt) outliers start: 58 outliers final: 45 residues processed: 431 average time/residue: 0.6971 time to fit residues: 482.0953 Evaluate side-chains 437 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 381 time to evaluate : 3.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 605 ARG Chi-restraints excluded: chain C residue 625 ASP Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 20 LYS Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 136 LYS Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain Q residue 19 MET Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain S residue 28 MET Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 38 THR Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain U residue 68 ARG Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain H residue 9 LYS Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 56 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 260 optimal weight: 0.9990 chunk 349 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 302 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 328 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 337 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 467 ASN ** C 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 85 ASN K 15 HIS ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.225268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.203017 restraints weight = 90930.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.196059 restraints weight = 117858.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.191272 restraints weight = 127431.244| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5849 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 55743 Z= 0.300 Angle : 0.778 11.757 81872 Z= 0.394 Chirality : 0.045 0.316 10277 Planarity : 0.006 0.128 5424 Dihedral : 24.154 178.746 24170 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.76 % Favored : 94.04 % Rotamer: Outliers : 3.23 % Allowed : 20.22 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.07 % 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: -0.84 (0.15), residues: 2884 helix: 0.62 (0.15), residues: 1140 sheet: -1.04 (0.22), residues: 531 loop : -1.43 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 18 HIS 0.008 0.002 HIS K 56 PHE 0.022 0.003 PHE C 418 TYR 0.026 0.003 TYR J 7 ARG 0.010 0.001 ARG S 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11620.65 seconds wall clock time: 210 minutes 56.07 seconds (12656.07 seconds total)