Starting phenix.real_space_refine on Wed Apr 17 06:07:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdv_16596/04_2024/8cdv_16596.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdv_16596/04_2024/8cdv_16596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdv_16596/04_2024/8cdv_16596.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdv_16596/04_2024/8cdv_16596.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdv_16596/04_2024/8cdv_16596.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cdv_16596/04_2024/8cdv_16596.pdb" } resolution = 4.73 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 1258 5.49 5 S 44 5.16 5 C 22451 2.51 5 N 8039 2.21 5 O 11801 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 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 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 "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 GLU 153": "OE1" <-> "OE2" Residue "F GLU 191": "OE1" <-> "OE2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "G ARG 32": "NH1" <-> "NH2" 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 "H GLU 60": "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 "I GLU 26": "OE1" <-> "OE2" Residue "I GLU 43": "OE1" <-> "OE2" Residue "I GLU 50": "OE1" <-> "OE2" Residue "I ARG 96": "NH1" <-> "NH2" Residue "I GLU 126": "OE1" <-> "OE2" Residue "J GLU 25": "OE1" <-> "OE2" Residue "J GLU 37": "OE1" <-> "OE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "J GLU 93": "OE1" <-> "OE2" Residue "J ARG 100": "NH1" <-> "NH2" Residue "K GLU 23": "OE1" <-> "OE2" Residue "K GLU 27": "OE1" <-> "OE2" Residue "K GLU 99": "OE1" <-> "OE2" Residue "L ARG 69": "NH1" <-> "NH2" Residue "L GLU 75": "OE1" <-> "OE2" Residue "M ARG 11": "NH1" <-> "NH2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "M GLU 66": "OE1" <-> "OE2" Residue "M GLU 72": "OE1" <-> "OE2" Residue "M GLU 82": "OE1" <-> "OE2" Residue "M ARG 87": "NH1" <-> "NH2" Residue "M ARG 107": "NH1" <-> "NH2" 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 "P PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 3": "OE1" <-> "OE2" Residue "R GLU 20": "OE1" <-> "OE2" Residue "R GLU 73": "OE1" <-> "OE2" Residue "S GLU 36": "OE1" <-> "OE2" Residue "S ARG 74": "NH1" <-> "NH2" Residue "S ARG 78": "NH1" <-> "NH2" Residue "T GLU 36": "OE1" <-> "OE2" Residue "T TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 51": "OE1" <-> "OE2" Residue "T ARG 56": "NH1" <-> "NH2" Residue "T GLU 93": "OE1" <-> "OE2" Residue "U GLU 40": "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" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 43593 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 26755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1247, 26755 Classifications: {'RNA': 1247} Modifications used: {'rna2p_pur': 97, 'rna2p_pyr': 64, 'rna3p_pur': 614, 'rna3p_pyr': 472} Link IDs: {'rna2p': 161, 'rna3p': 1085} Chain breaks: 4 Chain: "B" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 242 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 9} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "C" Number of atoms: 3687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3687 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 17, 'TRANS': 439} Chain breaks: 1 Chain: "F" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1490 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 2 Chain: "G" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1170 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 7, 'TRANS': 150} Chain: "H" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 727 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain breaks: 1 Chain: "I" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1036 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "J" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 776 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "K" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 489 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain breaks: 1 Chain: "L" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1052 Classifications: {'peptide': 136} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 128} Chain: "M" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 868 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "O" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 710 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "P" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 695 Classifications: {'peptide': 88} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 82} Chain: "Q" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 691 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "R" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 633 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "S" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 637 Classifications: {'peptide': 83} Link IDs: {'TRANS': 82} Chain: "T" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 755 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} 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: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 662 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Time building chain proxies: 21.98, per 1000 atoms: 0.50 Number of scatterers: 43593 At special positions: 0 Unit cell: (152.8, 220, 201.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 1258 15.00 O 11801 8.00 N 8039 7.00 C 22451 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 27.70 Conformation dependent library (CDL) restraints added in 3.1 seconds 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3900 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 21 sheets defined 48.7% alpha, 19.0% beta 342 base pairs and 689 stacking pairs defined. Time for finding SS restraints: 21.76 Creating SS restraints... Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 23 through 31 Processing helix chain 'C' and resid 35 through 52 Processing helix chain 'C' and resid 228 through 236 Processing helix chain 'C' and resid 241 through 246 Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.982A pdb=" N TYR C 293 " --> pdb=" O ASP C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 308 Processing helix chain 'C' and resid 322 through 327 Processing helix chain 'C' and resid 371 through 379 Processing helix chain 'C' and resid 382 through 389 Processing helix chain 'C' and resid 392 through 413 Processing helix chain 'C' and resid 442 through 467 Processing helix chain 'C' and resid 479 through 493 removed outlier: 3.519A pdb=" N THR C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 504 removed outlier: 4.340A pdb=" N ILE C 504 " --> pdb=" O ALA C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 517 removed outlier: 3.806A pdb=" N LEU C 509 " --> pdb=" O HIS C 505 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 512 " --> pdb=" O ALA C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 533 Processing helix chain 'C' and resid 545 through 549 Processing helix chain 'C' and resid 562 through 576 Processing helix chain 'C' and resid 582 through 616 Proline residue: C 594 - end of helix Processing helix chain 'F' and resid 7 through 16 removed outlier: 4.437A pdb=" N LEU F 11 " --> pdb=" O PRO F 7 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER F 12 " --> pdb=" O SER F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 62 Processing helix chain 'F' and resid 64 through 78 removed outlier: 3.822A pdb=" N LYS F 77 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.623A 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 116 Processing helix chain 'F' and resid 143 through 146 Processing helix chain 'F' and resid 148 through 154 Processing helix chain 'F' and resid 190 through 200 removed outlier: 3.649A pdb=" N ILE F 194 " --> pdb=" O ASN F 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 9 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 145 Processing helix chain 'G' and resid 149 through 158 Processing helix chain 'H' and resid 20 through 31 Processing helix chain 'H' and resid 35 through 55 removed outlier: 3.538A pdb=" N SER H 39 " --> pdb=" O LYS H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 69 Processing helix chain 'H' and resid 93 through 111 Processing helix chain 'H' and resid 115 through 128 Processing helix chain 'I' and resid 5 through 20 Processing helix chain 'I' and resid 30 through 43 Processing helix chain 'I' and resid 90 through 94 removed outlier: 3.555A pdb=" N VAL I 94 " --> pdb=" O SER I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 101 Processing helix chain 'I' and resid 115 through 121 Processing helix chain 'J' and resid 34 through 39 Processing helix chain 'J' and resid 41 through 55 Proline residue: J 51 - end of helix Processing helix chain 'J' and resid 71 through 91 removed outlier: 3.580A pdb=" N GLU J 89 " --> pdb=" O ARG J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 101 Processing helix chain 'K' and resid 14 through 32 Processing helix chain 'K' and resid 80 through 89 Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 21 through 24 Processing helix chain 'L' and resid 126 through 131 removed outlier: 3.683A pdb=" N GLY L 131 " --> pdb=" O SER L 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 20 removed outlier: 3.647A pdb=" N THR M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 44 through 48 Processing helix chain 'M' and resid 49 through 62 removed outlier: 3.797A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 83 Processing helix chain 'M' and resid 85 through 93 Processing helix chain 'O' and resid 5 through 16 Processing helix chain 'O' and resid 24 through 46 removed outlier: 3.649A 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 77 Processing helix chain 'P' and resid 78 through 89 removed outlier: 3.602A pdb=" N LYS P 87 " --> pdb=" O PHE P 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 25 Processing helix chain 'R' and resid 41 through 45 Processing helix chain 'R' and resid 63 through 67 Processing helix chain 'R' and resid 70 through 75 Processing helix chain 'S' and resid 5 through 41 removed outlier: 3.580A pdb=" N LYS S 9 " --> pdb=" O LYS S 5 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 64 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 35 Processing helix chain 'U' and resid 36 through 38 No H-bonds generated for 'chain 'U' and resid 36 through 38' 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 56 through 61 removed outlier: 4.007A pdb=" N SER V 60 " --> pdb=" O GLY V 56 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR V 61 " --> pdb=" O SER V 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 56 through 61' Processing helix chain 'V' and resid 61 through 80 removed outlier: 3.722A pdb=" N GLU V 78 " --> pdb=" O LYS V 74 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS V 79 " --> pdb=" O GLY V 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 93 through 105 removed outlier: 4.765A pdb=" N ALA V 97 " --> pdb=" O SER V 93 " (cutoff:3.500A) 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 249 through 250 removed outlier: 3.647A pdb=" N GLU C 355 " --> pdb=" O THR C 346 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 257 through 260 removed outlier: 6.038A pdb=" N THR C 258 " --> pdb=" O MET C 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 311 through 312 Processing sheet with id=AA5, first strand: chain 'C' and resid 422 through 427 removed outlier: 4.468A pdb=" N GLU C 422 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 472 through 474 Processing sheet with id=AA7, first strand: chain 'F' and resid 124 through 125 Processing sheet with id=AA8, first strand: chain 'G' and resid 12 through 25 removed outlier: 5.311A pdb=" N GLU G 13 " --> pdb=" O GLY G 40 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLY G 40 " --> pdb=" O GLU G 13 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU G 15 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL G 38 " --> pdb=" O LEU G 15 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 85 through 89 Processing sheet with id=AB1, first strand: chain 'I' and resid 24 through 28 removed outlier: 3.591A pdb=" N ASP I 48 " --> pdb=" O PHE I 63 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 76 through 79 Processing sheet with id=AB3, first strand: chain 'I' and resid 76 through 79 removed outlier: 5.424A pdb=" N VAL I 127 " --> pdb=" O SER I 107 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER I 107 " --> pdb=" O VAL I 127 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 6 through 12 removed outlier: 6.286A pdb=" N VAL J 29 " --> pdb=" O VAL J 65 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL J 67 " --> pdb=" O VAL J 29 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 71 through 75 Processing sheet with id=AB6, first strand: chain 'L' and resid 26 through 29 Processing sheet with id=AB7, first strand: chain 'L' and resid 42 through 53 removed outlier: 5.595A pdb=" N CYS L 47 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ARG L 69 " --> pdb=" O CYS L 47 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N TYR L 108 " --> pdb=" O GLU L 75 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR L 77 " --> pdb=" O TYR L 108 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE L 110 " --> pdb=" O THR L 77 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TYR L 79 " --> pdb=" O ILE L 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 48 through 51 removed outlier: 6.401A pdb=" N ILE P 20 " --> pdb=" O VAL P 37 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N THR P 39 " --> pdb=" O TYR P 18 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR P 18 " --> pdb=" O THR P 39 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASN P 41 " --> pdb=" O PRO P 16 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE P 17 " --> pdb=" O MET P 10 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Q' and resid 9 through 19 removed outlier: 16.739A pdb=" N VAL Q 9 " --> pdb=" O TYR Q 30 " (cutoff:3.500A) removed outlier: 13.694A pdb=" N TYR Q 30 " --> pdb=" O VAL Q 9 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN Q 11 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU Q 28 " --> pdb=" O GLN Q 11 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N THR Q 24 " --> pdb=" O VAL Q 15 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASP Q 17 " --> pdb=" O THR Q 22 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR Q 22 " --> pdb=" O ASP Q 17 " (cutoff:3.500A) removed outlier: 15.949A pdb=" N LYS Q 73 " --> pdb=" O SER Q 43 " (cutoff:3.500A) removed outlier: 13.312A pdb=" N LYS Q 45 " --> pdb=" O LYS Q 73 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N PHE Q 75 " --> pdb=" O LYS Q 45 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS Q 47 " --> pdb=" O PHE Q 75 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU Q 77 " --> pdb=" O LYS Q 47 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N HIS Q 49 " --> pdb=" O LEU Q 77 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N GLU Q 79 " --> pdb=" O HIS Q 49 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS Q 62 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL Q 80 " --> pdb=" O ILE Q 60 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE Q 60 " --> pdb=" O VAL Q 80 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'R' and resid 31 through 33 Processing sheet with id=AC2, first strand: chain 'T' and resid 36 through 52 removed outlier: 6.975A pdb=" N THR T 38 " --> pdb=" O GLN T 66 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N GLN T 66 " --> pdb=" O THR T 38 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR T 40 " --> pdb=" O ASN T 64 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASN T 64 " --> pdb=" O THR T 40 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ASP T 42 " --> pdb=" O ILE T 62 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE T 62 " --> pdb=" O ASP T 42 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY T 44 " --> pdb=" O TYR T 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR T 60 " --> pdb=" O GLY T 44 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG T 56 " --> pdb=" O LEU T 48 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG T 87 " --> pdb=" O ILE T 9 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'V' and resid 43 through 48 removed outlier: 6.887A pdb=" N ILE V 36 " --> pdb=" O ILE V 44 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TRP V 46 " --> pdb=" O VAL V 34 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL V 34 " --> pdb=" O TRP V 46 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER V 48 " --> pdb=" O THR V 32 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR V 32 " --> pdb=" O SER V 48 " (cutoff:3.500A) 893 hydrogen bonds defined for protein. 2526 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 842 hydrogen bonds 1332 hydrogen bond angles 0 basepair planarities 342 basepair parallelities 689 stacking parallelities Total time for adding SS restraints: 33.97 Time building geometry restraints manager: 28.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 3953 1.28 - 1.42: 17935 1.42 - 1.56: 22571 1.56 - 1.70: 2510 1.70 - 1.84: 84 Bond restraints: 47053 Sorted by residual: bond pdb=" C LYS P 13 " pdb=" O LYS P 13 " ideal model delta sigma weight residual 1.235 1.143 0.092 1.26e-02 6.30e+03 5.36e+01 bond pdb=" C SER K 94 " pdb=" O SER K 94 " ideal model delta sigma weight residual 1.235 1.161 0.074 1.26e-02 6.30e+03 3.50e+01 bond pdb=" O5' G A 764 " pdb=" C5' G A 764 " ideal model delta sigma weight residual 1.420 1.478 -0.058 1.50e-02 4.44e+03 1.50e+01 bond pdb=" O5' C A 668 " pdb=" C5' C A 668 " ideal model delta sigma weight residual 1.420 1.478 -0.058 1.50e-02 4.44e+03 1.47e+01 bond pdb=" O5' G A 736 " pdb=" C5' G A 736 " ideal model delta sigma weight residual 1.420 1.476 -0.056 1.50e-02 4.44e+03 1.40e+01 ... (remaining 47048 not shown) Histogram of bond angle deviations from ideal: 95.75 - 104.21: 4842 104.21 - 112.67: 27734 112.67 - 121.13: 24249 121.13 - 129.59: 12131 129.59 - 138.05: 793 Bond angle restraints: 69749 Sorted by residual: angle pdb=" CA LYS P 13 " pdb=" C LYS P 13 " pdb=" N LYS P 14 " ideal model delta sigma weight residual 116.84 129.59 -12.75 1.71e+00 3.42e-01 5.56e+01 angle pdb=" CB LYS S 81 " pdb=" CG LYS S 81 " pdb=" CD LYS S 81 " ideal model delta sigma weight residual 111.30 128.27 -16.97 2.30e+00 1.89e-01 5.44e+01 angle pdb=" CA SER K 94 " pdb=" C SER K 94 " pdb=" O SER K 94 " ideal model delta sigma weight residual 120.51 110.34 10.17 1.43e+00 4.89e-01 5.06e+01 angle pdb=" O3' G A1148 " pdb=" C3' G A1148 " pdb=" C2' G A1148 " ideal model delta sigma weight residual 109.50 119.27 -9.77 1.50e+00 4.44e-01 4.24e+01 angle pdb=" CA SER K 94 " pdb=" C SER K 94 " pdb=" N GLY K 95 " ideal model delta sigma weight residual 116.84 127.88 -11.04 1.71e+00 3.42e-01 4.17e+01 ... (remaining 69744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 26385 35.19 - 70.38: 3097 70.38 - 105.57: 489 105.57 - 140.76: 25 140.76 - 175.95: 24 Dihedral angle restraints: 30020 sinusoidal: 23990 harmonic: 6030 Sorted by residual: dihedral pdb=" CA ASP G 5 " pdb=" C ASP G 5 " pdb=" N PRO G 6 " pdb=" CA PRO G 6 " ideal model delta harmonic sigma weight residual -180.00 -126.42 -53.58 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CA LYS R 28 " pdb=" C LYS R 28 " pdb=" N GLN R 29 " pdb=" CA GLN R 29 " ideal model delta harmonic sigma weight residual -180.00 -130.21 -49.79 0 5.00e+00 4.00e-02 9.92e+01 dihedral pdb=" C4' G A 641 " pdb=" C3' G A 641 " pdb=" C2' G A 641 " pdb=" C1' G A 641 " ideal model delta sinusoidal sigma weight residual -35.00 33.54 -68.54 1 8.00e+00 1.56e-02 9.51e+01 ... (remaining 30017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 6102 0.122 - 0.244: 2597 0.244 - 0.366: 148 0.366 - 0.488: 7 0.488 - 0.610: 7 Chirality restraints: 8861 Sorted by residual: chirality pdb=" P A B -1 " pdb=" OP1 A B -1 " pdb=" OP2 A B -1 " pdb=" O5' A B -1 " both_signs ideal model delta sigma weight residual True 2.41 3.02 -0.61 2.00e-01 2.50e+01 9.30e+00 chirality pdb=" P C A 815 " pdb=" OP1 C A 815 " pdb=" OP2 C A 815 " pdb=" O5' C A 815 " both_signs ideal model delta sigma weight residual True 2.41 -3.00 -0.59 2.00e-01 2.50e+01 8.67e+00 chirality pdb=" P G A 8 " pdb=" OP1 G A 8 " pdb=" OP2 G A 8 " pdb=" O5' G A 8 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.57 2.00e-01 2.50e+01 8.26e+00 ... (remaining 8858 not shown) Planarity restraints: 4164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 89 " 1.019 9.50e-02 1.11e+02 4.57e-01 1.27e+02 pdb=" NE ARG K 89 " -0.068 2.00e-02 2.50e+03 pdb=" CZ ARG K 89 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG K 89 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG K 89 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 39 " -0.925 9.50e-02 1.11e+02 4.15e-01 1.12e+02 pdb=" NE ARG Q 39 " 0.073 2.00e-02 2.50e+03 pdb=" CZ ARG Q 39 " -0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 39 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 39 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 78 " -0.918 9.50e-02 1.11e+02 4.12e-01 1.07e+02 pdb=" NE ARG R 78 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG R 78 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG R 78 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG R 78 " -0.012 2.00e-02 2.50e+03 ... (remaining 4161 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 4 1.93 - 2.67: 2293 2.67 - 3.41: 62382 3.41 - 4.16: 147745 4.16 - 4.90: 206452 Nonbonded interactions: 418876 Sorted by model distance: nonbonded pdb=" O2' G A 641 " pdb=" OP1 U A 642 " model vdw 1.187 2.440 nonbonded pdb=" C5' A B 6 " pdb=" N3 A B 6 " model vdw 1.659 3.520 nonbonded pdb=" O5' A B 6 " pdb=" N3 A B 6 " model vdw 1.808 3.120 nonbonded pdb=" O2' U A1198 " pdb=" OP1 G A1199 " model vdw 1.920 2.440 nonbonded pdb=" OP1 U A 64 " pdb=" O2' U A 393 " model vdw 1.972 2.440 ... (remaining 418871 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: 4.660 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: 0.030 Extract box with map and model: 14.180 Check model and map are aligned: 0.560 Set scattering table: 0.370 Process input model: 148.540 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 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 0.092 47053 Z= 0.563 Angle : 1.435 16.966 69749 Z= 0.900 Chirality : 0.114 0.610 8861 Planarity : 0.025 0.457 4164 Dihedral : 24.687 175.951 26120 Min Nonbonded Distance : 1.187 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.93 % Allowed : 3.02 % Favored : 96.05 % Rotamer: Outliers : 3.68 % Allowed : 5.24 % Favored : 91.09 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.10 % 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: -1.91 (0.16), residues: 2050 helix: -1.21 (0.14), residues: 916 sheet: -1.55 (0.24), residues: 364 loop : -0.87 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.005 TRP P 59 HIS 0.042 0.004 HIS S 20 PHE 0.052 0.007 PHE C 463 TYR 0.096 0.008 TYR U 17 ARG 0.048 0.004 ARG J 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 656 time to evaluate : 2.615 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 PHE cc_start: 0.5327 (t80) cc_final: 0.5066 (t80) REVERT: C 267 LEU cc_start: 0.6066 (mt) cc_final: 0.5600 (mp) REVERT: C 367 GLU cc_start: 0.5685 (tp30) cc_final: 0.5464 (mp0) REVERT: C 407 ARG cc_start: 0.4453 (ttt180) cc_final: 0.3880 (mtm180) REVERT: C 472 TYR cc_start: 0.3319 (m-80) cc_final: 0.3106 (m-80) REVERT: C 525 ILE cc_start: 0.6422 (mt) cc_final: 0.6060 (mt) REVERT: C 535 GLN cc_start: 0.5041 (mt0) cc_final: 0.4492 (mm-40) REVERT: C 538 TYR cc_start: 0.5257 (m-80) cc_final: 0.4683 (m-10) REVERT: C 541 GLN cc_start: 0.4968 (mt0) cc_final: 0.4450 (mt0) REVERT: C 604 GLU cc_start: 0.5524 (tt0) cc_final: 0.4960 (mm-30) REVERT: F 24 LYS cc_start: 0.6273 (pttm) cc_final: 0.5902 (mttm) REVERT: F 66 ARG cc_start: 0.6163 (OUTLIER) cc_final: 0.5827 (tpp-160) REVERT: F 90 LEU cc_start: 0.7827 (mt) cc_final: 0.7435 (mp) REVERT: F 91 ASP cc_start: 0.7431 (t70) cc_final: 0.7202 (t0) REVERT: F 142 ARG cc_start: 0.6685 (ptt180) cc_final: 0.6170 (ptp-170) REVERT: F 164 TYR cc_start: 0.6819 (p90) cc_final: 0.6425 (p90) REVERT: F 179 LEU cc_start: 0.7700 (mt) cc_final: 0.7448 (pp) REVERT: F 191 GLU cc_start: 0.7900 (pm20) cc_final: 0.7545 (pm20) REVERT: G 64 VAL cc_start: 0.4542 (t) cc_final: 0.4206 (p) REVERT: G 69 LYS cc_start: 0.6664 (mptt) cc_final: 0.6446 (mttt) REVERT: G 70 ASN cc_start: 0.6833 (m-40) cc_final: 0.6631 (p0) REVERT: G 96 LEU cc_start: 0.7618 (mt) cc_final: 0.7330 (mt) REVERT: G 105 VAL cc_start: 0.7561 (t) cc_final: 0.7295 (t) REVERT: G 132 THR cc_start: 0.7021 (m) cc_final: 0.6714 (p) REVERT: G 141 LEU cc_start: 0.7083 (mt) cc_final: 0.6638 (mt) REVERT: G 152 ASP cc_start: 0.4062 (m-30) cc_final: 0.3426 (p0) REVERT: G 157 ARG cc_start: 0.4864 (OUTLIER) cc_final: 0.4520 (mtt-85) REVERT: H 114 LYS cc_start: 0.6989 (mttt) cc_final: 0.6555 (tttm) REVERT: I 25 LEU cc_start: 0.7438 (pt) cc_final: 0.7235 (pt) REVERT: I 35 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8402 (tp30) REVERT: I 51 PHE cc_start: 0.8349 (m-80) cc_final: 0.8069 (m-10) REVERT: I 66 TYR cc_start: 0.5691 (m-80) cc_final: 0.5468 (m-80) REVERT: I 99 ASN cc_start: 0.7767 (t0) cc_final: 0.7553 (t0) REVERT: J 12 ARG cc_start: 0.4946 (OUTLIER) cc_final: 0.4726 (ttm170) REVERT: J 25 GLU cc_start: 0.3613 (OUTLIER) cc_final: 0.3398 (pp20) REVERT: K 87 LEU cc_start: 0.3307 (mt) cc_final: 0.3054 (mp) REVERT: K 89 ARG cc_start: 0.3006 (OUTLIER) cc_final: 0.2740 (mtt90) REVERT: L 21 SER cc_start: 0.5209 (m) cc_final: 0.4947 (t) REVERT: L 47 CYS cc_start: 0.7130 (m) cc_final: 0.6278 (t) REVERT: L 50 VAL cc_start: 0.6833 (t) cc_final: 0.5662 (p) REVERT: L 54 THR cc_start: 0.7077 (p) cc_final: 0.6426 (t) REVERT: L 67 ARG cc_start: 0.5379 (tpt170) cc_final: 0.4966 (ttt-90) REVERT: L 75 GLU cc_start: 0.7424 (tt0) cc_final: 0.6718 (pm20) REVERT: L 77 THR cc_start: 0.7814 (m) cc_final: 0.6688 (p) REVERT: L 103 LEU cc_start: 0.6827 (mt) cc_final: 0.6615 (tp) REVERT: L 111 VAL cc_start: 0.7145 (t) cc_final: 0.6902 (p) REVERT: L 136 LYS cc_start: 0.6422 (OUTLIER) cc_final: 0.6146 (tttt) REVERT: M 97 VAL cc_start: 0.1882 (OUTLIER) cc_final: 0.1610 (m) REVERT: O 6 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: O 7 ARG cc_start: 0.7345 (tpt170) cc_final: 0.6355 (tpt170) REVERT: O 20 SER cc_start: 0.6680 (p) cc_final: 0.6432 (t) REVERT: O 69 TYR cc_start: 0.8090 (t80) cc_final: 0.7680 (t80) REVERT: O 72 ASN cc_start: 0.8293 (m110) cc_final: 0.8086 (m-40) REVERT: O 74 ASP cc_start: 0.3522 (t0) cc_final: 0.3271 (t0) REVERT: O 82 ILE cc_start: 0.8460 (pt) cc_final: 0.8153 (tt) REVERT: P 54 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8004 (mm-30) REVERT: P 77 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7550 (tp40) REVERT: Q 5 ASN cc_start: 0.8401 (m-40) cc_final: 0.8197 (m110) REVERT: Q 17 ASP cc_start: 0.6433 (p0) cc_final: 0.6120 (t0) REVERT: Q 24 THR cc_start: 0.6333 (m) cc_final: 0.5816 (p) REVERT: Q 63 ILE cc_start: 0.8178 (pt) cc_final: 0.7941 (pt) REVERT: R 16 MET cc_start: 0.2413 (tpp) cc_final: -0.0058 (tmm) REVERT: R 62 ILE cc_start: 0.6475 (mm) cc_final: 0.6162 (mp) REVERT: R 81 LYS cc_start: 0.2042 (OUTLIER) cc_final: 0.1774 (mmtp) REVERT: S 25 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.7122 (tttt) REVERT: S 29 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7399 (mmp-170) REVERT: S 66 LEU cc_start: 0.6403 (tp) cc_final: 0.6180 (tp) REVERT: T 5 GLU cc_start: 0.7494 (tt0) cc_final: 0.7166 (tm-30) REVERT: T 26 PHE cc_start: 0.7152 (m-80) cc_final: 0.6802 (m-10) REVERT: T 41 LYS cc_start: 0.7142 (mttt) cc_final: 0.6907 (tptt) REVERT: T 52 ILE cc_start: 0.7730 (mt) cc_final: 0.7433 (tp) REVERT: T 87 ARG cc_start: 0.4207 (OUTLIER) cc_final: 0.3729 (ttm-80) REVERT: T 93 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7514 (mm-30) REVERT: U 27 ASP cc_start: 0.5584 (t70) cc_final: 0.5190 (t70) REVERT: U 33 LEU cc_start: 0.6158 (tp) cc_final: 0.5881 (tt) REVERT: U 60 LEU cc_start: 0.7948 (tp) cc_final: 0.7622 (tp) REVERT: U 61 THR cc_start: 0.7586 (m) cc_final: 0.7253 (m) REVERT: U 64 ILE cc_start: 0.8346 (mt) cc_final: 0.8032 (mp) REVERT: U 65 LYS cc_start: 0.8317 (mttt) cc_final: 0.8113 (mttt) REVERT: U 75 TYR cc_start: 0.8162 (m-80) cc_final: 0.7962 (m-80) REVERT: V 27 SER cc_start: 0.7421 (t) cc_final: 0.7146 (m) outliers start: 66 outliers final: 12 residues processed: 696 average time/residue: 0.6672 time to fit residues: 717.3890 Evaluate side-chains 423 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 399 time to evaluate : 2.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 275 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 255 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 190 optimal weight: 0.7980 chunk 296 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 HIS C 535 GLN F 64 ASN F 67 GLN F 112 GLN ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN G 70 ASN H 56 ASN H 64 GLN H 106 ASN H 122 ASN ** I 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 ASN L 5 ASN ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 ASN O 18 HIS O 37 ASN O 72 ASN ** O 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 72 ASN R 47 HIS R 57 HIS T 33 ASN T 61 GLN ** V 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 66 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 47053 Z= 0.298 Angle : 0.857 10.198 69749 Z= 0.445 Chirality : 0.049 0.355 8861 Planarity : 0.006 0.081 4164 Dihedral : 25.196 177.848 21890 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 24.06 Ramachandran Plot: Outliers : 0.29 % Allowed : 1.80 % Favored : 97.90 % Rotamer: Outliers : 0.33 % Allowed : 3.96 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.18), residues: 2050 helix: 0.79 (0.16), residues: 937 sheet: -0.73 (0.27), residues: 331 loop : -0.42 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP T 43 HIS 0.007 0.002 HIS S 20 PHE 0.026 0.003 PHE U 18 TYR 0.024 0.003 TYR Q 36 ARG 0.007 0.001 ARG C 439 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 466 time to evaluate : 2.835 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 PHE cc_start: 0.5736 (t80) cc_final: 0.5340 (t80) REVERT: C 312 TYR cc_start: 0.3941 (m-80) cc_final: 0.3539 (m-80) REVERT: C 404 GLN cc_start: 0.4918 (mt0) cc_final: 0.4486 (mt0) REVERT: C 407 ARG cc_start: 0.4489 (ttt180) cc_final: 0.3874 (mtm180) REVERT: C 538 TYR cc_start: 0.5170 (m-80) cc_final: 0.4889 (m-10) REVERT: C 563 TYR cc_start: 0.4842 (t80) cc_final: 0.4518 (t80) REVERT: C 604 GLU cc_start: 0.5587 (tt0) cc_final: 0.5260 (mm-30) REVERT: F 86 PHE cc_start: 0.7505 (t80) cc_final: 0.7093 (t80) REVERT: F 87 MET cc_start: 0.8667 (mmm) cc_final: 0.8373 (mmm) REVERT: F 91 ASP cc_start: 0.7406 (t70) cc_final: 0.7105 (p0) REVERT: F 111 ARG cc_start: 0.7082 (ttt-90) cc_final: 0.6725 (ttt-90) REVERT: F 125 ARG cc_start: 0.5687 (ttt180) cc_final: 0.5012 (mtt180) REVERT: F 146 ARG cc_start: 0.5744 (mtp180) cc_final: 0.5543 (ttp80) REVERT: F 147 ASN cc_start: 0.8117 (p0) cc_final: 0.7804 (p0) REVERT: F 164 TYR cc_start: 0.7250 (p90) cc_final: 0.6827 (p90) REVERT: F 168 ASP cc_start: 0.4707 (t0) cc_final: 0.3843 (t70) REVERT: G 96 LEU cc_start: 0.7525 (mt) cc_final: 0.7253 (mt) REVERT: G 112 ARG cc_start: 0.6634 (tpp80) cc_final: 0.6268 (mmm-85) REVERT: G 132 THR cc_start: 0.7433 (m) cc_final: 0.6924 (p) REVERT: H 114 LYS cc_start: 0.7045 (mttt) cc_final: 0.6757 (tttm) REVERT: I 35 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8502 (tp30) REVERT: I 45 PHE cc_start: 0.7583 (m-80) cc_final: 0.6936 (m-80) REVERT: I 66 TYR cc_start: 0.5428 (m-80) cc_final: 0.4730 (m-80) REVERT: J 12 ARG cc_start: 0.4676 (tpt-90) cc_final: 0.4389 (ttm170) REVERT: L 21 SER cc_start: 0.5552 (m) cc_final: 0.4986 (t) REVERT: L 53 MET cc_start: 0.6495 (tpt) cc_final: 0.6064 (ttt) REVERT: L 54 THR cc_start: 0.7939 (p) cc_final: 0.7386 (p) REVERT: L 75 GLU cc_start: 0.7110 (tt0) cc_final: 0.6437 (pm20) REVERT: L 76 VAL cc_start: 0.7609 (m) cc_final: 0.7027 (t) REVERT: L 77 THR cc_start: 0.7686 (m) cc_final: 0.6173 (p) REVERT: L 106 VAL cc_start: 0.7198 (p) cc_final: 0.6975 (m) REVERT: L 132 THR cc_start: 0.8352 (m) cc_final: 0.8061 (p) REVERT: L 136 LYS cc_start: 0.5721 (tptt) cc_final: 0.5493 (tttt) REVERT: M 59 ILE cc_start: 0.3724 (OUTLIER) cc_final: 0.3279 (tp) REVERT: O 46 HIS cc_start: 0.6760 (m90) cc_final: 0.6540 (m90) REVERT: Q 18 LYS cc_start: 0.8130 (mttt) cc_final: 0.7846 (tppt) REVERT: R 49 ILE cc_start: 0.4945 (mt) cc_final: 0.4742 (mt) REVERT: S 29 ARG cc_start: 0.7648 (mtt90) cc_final: 0.7345 (mmp80) REVERT: S 71 THR cc_start: 0.7717 (m) cc_final: 0.6780 (m) REVERT: S 75 TYR cc_start: 0.7209 (m-10) cc_final: 0.6925 (m-80) REVERT: T 5 GLU cc_start: 0.7375 (tt0) cc_final: 0.6989 (tm-30) REVERT: T 11 ARG cc_start: 0.6651 (ptp-170) cc_final: 0.6419 (ptp-170) REVERT: T 26 PHE cc_start: 0.7073 (m-80) cc_final: 0.6857 (m-10) REVERT: T 47 ARG cc_start: 0.7200 (mmm-85) cc_final: 0.6848 (mmm160) REVERT: T 60 TYR cc_start: 0.7106 (m-80) cc_final: 0.6760 (m-10) REVERT: U 75 TYR cc_start: 0.8102 (m-80) cc_final: 0.7895 (m-80) outliers start: 6 outliers final: 1 residues processed: 469 average time/residue: 0.6123 time to fit residues: 461.9769 Evaluate side-chains 346 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 344 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 164 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 246 optimal weight: 0.7980 chunk 201 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 296 optimal weight: 8.9990 chunk 320 optimal weight: 7.9990 chunk 264 optimal weight: 9.9990 chunk 294 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 chunk 237 optimal weight: 9.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN F 67 GLN I 69 ASN I 92 ASN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 ASN O 72 ASN ** R 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 HIS ** V 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 47053 Z= 0.289 Angle : 0.785 8.854 69749 Z= 0.409 Chirality : 0.045 0.291 8861 Planarity : 0.007 0.089 4164 Dihedral : 25.023 179.759 21890 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.78 % Favored : 96.98 % Rotamer: Outliers : 0.28 % Allowed : 4.85 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.16 (0.18), residues: 2050 helix: 0.58 (0.16), residues: 939 sheet: -0.48 (0.27), residues: 319 loop : -0.61 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP T 43 HIS 0.014 0.002 HIS C 599 PHE 0.028 0.003 PHE R 74 TYR 0.021 0.002 TYR L 108 ARG 0.027 0.001 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 441 time to evaluate : 2.742 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 69 MET cc_start: 0.2151 (tmm) cc_final: 0.1802 (tmm) REVERT: C 407 ARG cc_start: 0.4342 (ttt180) cc_final: 0.3716 (mtm180) REVERT: C 518 ASP cc_start: 0.3707 (m-30) cc_final: 0.3341 (t0) REVERT: C 538 TYR cc_start: 0.5427 (m-80) cc_final: 0.5157 (m-10) REVERT: C 563 TYR cc_start: 0.4646 (t80) cc_final: 0.4205 (t80) REVERT: F 7 PRO cc_start: 0.6028 (Cg_exo) cc_final: 0.5409 (Cg_endo) REVERT: F 47 TYR cc_start: 0.7288 (t80) cc_final: 0.6842 (t80) REVERT: F 91 ASP cc_start: 0.7423 (t70) cc_final: 0.7127 (p0) REVERT: F 98 VAL cc_start: 0.7938 (t) cc_final: 0.7684 (m) REVERT: F 125 ARG cc_start: 0.5523 (ttt180) cc_final: 0.5038 (mtt180) REVERT: G 96 LEU cc_start: 0.7564 (mt) cc_final: 0.7332 (mt) REVERT: G 127 SER cc_start: 0.6907 (t) cc_final: 0.6630 (p) REVERT: G 132 THR cc_start: 0.7280 (m) cc_final: 0.6840 (p) REVERT: H 114 LYS cc_start: 0.6742 (mttt) cc_final: 0.6500 (tttm) REVERT: I 103 ILE cc_start: 0.8567 (pt) cc_final: 0.8272 (mp) REVERT: J 12 ARG cc_start: 0.4536 (tpt-90) cc_final: 0.4189 (ttm170) REVERT: L 21 SER cc_start: 0.5346 (m) cc_final: 0.4951 (t) REVERT: L 53 MET cc_start: 0.6752 (tpt) cc_final: 0.6325 (ttt) REVERT: L 54 THR cc_start: 0.8171 (p) cc_final: 0.7592 (p) REVERT: L 75 GLU cc_start: 0.7365 (tt0) cc_final: 0.6868 (mt-10) REVERT: L 76 VAL cc_start: 0.7490 (m) cc_final: 0.7175 (t) REVERT: L 77 THR cc_start: 0.7412 (m) cc_final: 0.6182 (p) REVERT: L 95 ILE cc_start: 0.7993 (pt) cc_final: 0.7756 (pt) REVERT: M 59 ILE cc_start: 0.3859 (OUTLIER) cc_final: 0.3548 (tp) REVERT: O 46 HIS cc_start: 0.7005 (m90) cc_final: 0.6758 (m90) REVERT: Q 17 ASP cc_start: 0.7328 (p0) cc_final: 0.6445 (t0) REVERT: Q 18 LYS cc_start: 0.8066 (mttt) cc_final: 0.7622 (tptt) REVERT: R 43 GLN cc_start: 0.5674 (mt0) cc_final: 0.4836 (pm20) REVERT: R 49 ILE cc_start: 0.4450 (mt) cc_final: 0.4149 (mt) REVERT: R 79 THR cc_start: 0.5276 (m) cc_final: 0.5033 (m) REVERT: S 29 ARG cc_start: 0.7843 (mtt90) cc_final: 0.7585 (mmp80) REVERT: S 75 TYR cc_start: 0.7045 (m-10) cc_final: 0.6808 (m-80) REVERT: T 9 ILE cc_start: 0.5772 (mt) cc_final: 0.5524 (mt) REVERT: T 47 ARG cc_start: 0.7056 (mmm-85) cc_final: 0.6850 (mmm160) REVERT: T 60 TYR cc_start: 0.7230 (m-80) cc_final: 0.6809 (m-10) REVERT: U 16 CYS cc_start: 0.7546 (t) cc_final: 0.7301 (t) REVERT: U 75 TYR cc_start: 0.7636 (m-80) cc_final: 0.7226 (m-80) REVERT: V 67 MET cc_start: 0.3999 (ttm) cc_final: 0.3285 (tmm) outliers start: 5 outliers final: 0 residues processed: 443 average time/residue: 0.6321 time to fit residues: 444.4574 Evaluate side-chains 337 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 336 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 293 optimal weight: 1.9990 chunk 222 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 199 optimal weight: 0.4980 chunk 297 optimal weight: 1.9990 chunk 315 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 282 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 541 GLN F 59 HIS F 64 ASN F 67 GLN G 142 GLN I 22 HIS M 32 GLN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 101 ASN ** O 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 47053 Z= 0.170 Angle : 0.641 7.766 69749 Z= 0.337 Chirality : 0.039 0.293 8861 Planarity : 0.005 0.050 4164 Dihedral : 24.807 179.982 21890 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.90 % Favored : 97.85 % Rotamer: Outliers : 0.17 % Allowed : 2.62 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.33 (0.18), residues: 2050 helix: 1.05 (0.16), residues: 931 sheet: -0.39 (0.27), residues: 329 loop : -0.37 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP V 46 HIS 0.017 0.001 HIS R 14 PHE 0.018 0.002 PHE F 86 TYR 0.028 0.002 TYR I 130 ARG 0.014 0.001 ARG I 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 431 time to evaluate : 2.707 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 69 MET cc_start: 0.2285 (tmm) cc_final: 0.1864 (tmm) REVERT: C 345 MET cc_start: 0.2589 (ttm) cc_final: 0.1317 (mpp) REVERT: C 407 ARG cc_start: 0.4417 (ttt180) cc_final: 0.3834 (mtm180) REVERT: C 472 TYR cc_start: 0.3617 (m-10) cc_final: 0.3334 (m-80) REVERT: C 518 ASP cc_start: 0.3789 (m-30) cc_final: 0.3324 (t0) REVERT: C 563 TYR cc_start: 0.4607 (t80) cc_final: 0.4404 (t80) REVERT: C 596 ILE cc_start: 0.3402 (tp) cc_final: 0.2980 (tp) REVERT: F 72 PHE cc_start: 0.8206 (t80) cc_final: 0.7927 (t80) REVERT: F 91 ASP cc_start: 0.7404 (t70) cc_final: 0.7064 (p0) REVERT: F 125 ARG cc_start: 0.5662 (ttt180) cc_final: 0.5130 (mtt180) REVERT: G 96 LEU cc_start: 0.7421 (mt) cc_final: 0.7179 (mt) REVERT: G 127 SER cc_start: 0.6998 (t) cc_final: 0.6700 (p) REVERT: G 132 THR cc_start: 0.7371 (m) cc_final: 0.6958 (p) REVERT: H 114 LYS cc_start: 0.6465 (mttt) cc_final: 0.6235 (tttm) REVERT: J 12 ARG cc_start: 0.4592 (tpt-90) cc_final: 0.4224 (ttm170) REVERT: L 21 SER cc_start: 0.5531 (m) cc_final: 0.5068 (t) REVERT: L 54 THR cc_start: 0.8388 (p) cc_final: 0.7770 (t) REVERT: L 75 GLU cc_start: 0.7282 (tt0) cc_final: 0.6857 (mt-10) REVERT: L 76 VAL cc_start: 0.7613 (m) cc_final: 0.7353 (t) REVERT: L 77 THR cc_start: 0.7549 (m) cc_final: 0.6321 (p) REVERT: O 43 LEU cc_start: 0.7344 (pp) cc_final: 0.7143 (pp) REVERT: O 53 ARG cc_start: 0.7478 (mtp85) cc_final: 0.6509 (tpt170) REVERT: P 18 TYR cc_start: 0.7427 (m-80) cc_final: 0.7187 (m-80) REVERT: Q 17 ASP cc_start: 0.7274 (p0) cc_final: 0.6787 (m-30) REVERT: Q 18 LYS cc_start: 0.8144 (mttt) cc_final: 0.7598 (tptp) REVERT: Q 79 GLU cc_start: 0.6689 (tp30) cc_final: 0.5904 (pt0) REVERT: R 43 GLN cc_start: 0.5675 (mt0) cc_final: 0.5003 (pm20) REVERT: R 49 ILE cc_start: 0.4483 (mt) cc_final: 0.4203 (mt) REVERT: R 79 THR cc_start: 0.5375 (m) cc_final: 0.5053 (m) REVERT: S 29 ARG cc_start: 0.7853 (mtt90) cc_final: 0.7547 (mmp80) REVERT: S 39 VAL cc_start: 0.7731 (p) cc_final: 0.7527 (p) REVERT: T 9 ILE cc_start: 0.5939 (mt) cc_final: 0.5718 (mt) REVERT: T 60 TYR cc_start: 0.7392 (m-80) cc_final: 0.7066 (m-10) REVERT: U 64 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8080 (mp) REVERT: V 46 TRP cc_start: 0.2135 (p90) cc_final: 0.1207 (p90) REVERT: V 108 GLU cc_start: 0.6268 (mm-30) cc_final: 0.5956 (pm20) outliers start: 3 outliers final: 1 residues processed: 432 average time/residue: 0.6187 time to fit residues: 425.6704 Evaluate side-chains 345 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 343 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 262 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 234 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 268 optimal weight: 2.9990 chunk 217 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 282 optimal weight: 0.0010 chunk 79 optimal weight: 10.0000 overall best weight: 3.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 286 HIS ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN F 67 GLN F 112 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 ASN ** O 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN ** V 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 47053 Z= 0.278 Angle : 0.753 11.109 69749 Z= 0.386 Chirality : 0.043 0.309 8861 Planarity : 0.006 0.057 4164 Dihedral : 24.857 179.499 21890 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.61 % Favored : 96.15 % Rotamer: Outliers : 0.17 % Allowed : 4.12 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.18), residues: 2050 helix: 0.61 (0.16), residues: 921 sheet: -0.42 (0.28), residues: 310 loop : -0.60 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP T 43 HIS 0.015 0.002 HIS C 599 PHE 0.025 0.003 PHE C 418 TYR 0.042 0.003 TYR S 75 ARG 0.007 0.001 ARG G 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 409 time to evaluate : 2.716 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 69 MET cc_start: 0.2209 (tmm) cc_final: 0.1773 (tmm) REVERT: C 399 MET cc_start: 0.1084 (ttm) cc_final: 0.0440 (tmm) REVERT: C 407 ARG cc_start: 0.4210 (ttt180) cc_final: 0.3506 (mtm180) REVERT: C 518 ASP cc_start: 0.3648 (m-30) cc_final: 0.3158 (t0) REVERT: C 560 ILE cc_start: 0.6361 (mp) cc_final: 0.6050 (mp) REVERT: C 563 TYR cc_start: 0.4960 (t80) cc_final: 0.4454 (t80) REVERT: F 91 ASP cc_start: 0.7497 (t70) cc_final: 0.7108 (p0) REVERT: F 125 ARG cc_start: 0.5764 (ttt180) cc_final: 0.5248 (mtt180) REVERT: G 10 GLU cc_start: 0.7221 (mt-10) cc_final: 0.7015 (tm-30) REVERT: G 127 SER cc_start: 0.6977 (t) cc_final: 0.6653 (p) REVERT: G 132 THR cc_start: 0.7076 (m) cc_final: 0.6638 (p) REVERT: H 30 MET cc_start: 0.5342 (ptp) cc_final: 0.5095 (ttp) REVERT: I 63 PHE cc_start: 0.7062 (m-80) cc_final: 0.6408 (t80) REVERT: I 66 TYR cc_start: 0.5398 (m-80) cc_final: 0.4532 (m-10) REVERT: I 132 TRP cc_start: 0.8223 (p90) cc_final: 0.7443 (p90) REVERT: J 12 ARG cc_start: 0.4528 (tpt-90) cc_final: 0.4197 (ttm170) REVERT: J 98 LEU cc_start: 0.6119 (mm) cc_final: 0.5772 (tp) REVERT: L 21 SER cc_start: 0.5337 (m) cc_final: 0.5107 (t) REVERT: L 54 THR cc_start: 0.8424 (p) cc_final: 0.8188 (p) REVERT: L 55 PRO cc_start: 0.7792 (Cg_endo) cc_final: 0.7385 (Cg_exo) REVERT: L 75 GLU cc_start: 0.7178 (tt0) cc_final: 0.6819 (pm20) REVERT: L 77 THR cc_start: 0.7548 (m) cc_final: 0.6427 (p) REVERT: L 95 ILE cc_start: 0.8093 (pt) cc_final: 0.7871 (pt) REVERT: O 45 THR cc_start: 0.8329 (p) cc_final: 0.8116 (p) REVERT: O 53 ARG cc_start: 0.7626 (mtp85) cc_final: 0.6589 (tpt170) REVERT: P 80 MET cc_start: 0.6914 (mmm) cc_final: 0.6590 (mmt) REVERT: Q 17 ASP cc_start: 0.7307 (p0) cc_final: 0.6687 (m-30) REVERT: Q 18 LYS cc_start: 0.8078 (mttt) cc_final: 0.7578 (tptp) REVERT: R 49 ILE cc_start: 0.4376 (mt) cc_final: 0.4083 (mt) REVERT: R 79 THR cc_start: 0.5554 (m) cc_final: 0.5260 (m) REVERT: S 29 ARG cc_start: 0.7900 (mtt90) cc_final: 0.7600 (mmp80) REVERT: T 50 TYR cc_start: 0.6586 (p90) cc_final: 0.6169 (p90) REVERT: T 60 TYR cc_start: 0.7380 (m-80) cc_final: 0.6902 (m-80) REVERT: U 75 TYR cc_start: 0.7606 (m-80) cc_final: 0.7102 (m-80) REVERT: V 46 TRP cc_start: 0.1715 (p90) cc_final: 0.0667 (p90) outliers start: 3 outliers final: 0 residues processed: 409 average time/residue: 0.6045 time to fit residues: 397.1272 Evaluate side-chains 323 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 106 optimal weight: 20.0000 chunk 283 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 185 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 315 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 104 optimal weight: 20.0000 chunk 165 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 484 GLN F 64 ASN F 67 GLN F 112 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 47053 Z= 0.280 Angle : 0.750 10.525 69749 Z= 0.385 Chirality : 0.043 0.327 8861 Planarity : 0.006 0.093 4164 Dihedral : 24.904 179.666 21890 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.85 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.46 (0.18), residues: 2050 helix: 0.38 (0.16), residues: 917 sheet: -0.61 (0.27), residues: 315 loop : -0.83 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 9 HIS 0.008 0.002 HIS G 83 PHE 0.026 0.003 PHE U 18 TYR 0.046 0.003 TYR C 371 ARG 0.010 0.001 ARG G 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 2.822 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 69 MET cc_start: 0.2999 (tmm) cc_final: 0.2633 (tmm) REVERT: C 358 ILE cc_start: 0.4061 (mt) cc_final: 0.3808 (mt) REVERT: C 407 ARG cc_start: 0.4240 (ttt180) cc_final: 0.3597 (mtm180) REVERT: C 495 TYR cc_start: 0.2184 (m-80) cc_final: 0.1473 (m-80) REVERT: C 560 ILE cc_start: 0.6192 (mp) cc_final: 0.5842 (mp) REVERT: C 563 TYR cc_start: 0.4978 (t80) cc_final: 0.4338 (t80) REVERT: F 91 ASP cc_start: 0.7558 (t70) cc_final: 0.7159 (p0) REVERT: F 125 ARG cc_start: 0.5662 (ttt180) cc_final: 0.5130 (mtt180) REVERT: G 10 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6865 (pm20) REVERT: G 127 SER cc_start: 0.7024 (t) cc_final: 0.6720 (p) REVERT: G 130 SER cc_start: 0.6823 (t) cc_final: 0.6284 (t) REVERT: G 132 THR cc_start: 0.7240 (m) cc_final: 0.6858 (p) REVERT: I 66 TYR cc_start: 0.5695 (m-80) cc_final: 0.4907 (m-10) REVERT: J 12 ARG cc_start: 0.4346 (tpt-90) cc_final: 0.4016 (ttm170) REVERT: J 98 LEU cc_start: 0.6414 (mm) cc_final: 0.5979 (tp) REVERT: L 26 LYS cc_start: 0.7938 (mmtm) cc_final: 0.7476 (mptt) REVERT: L 54 THR cc_start: 0.8555 (p) cc_final: 0.7827 (t) REVERT: L 55 PRO cc_start: 0.7648 (Cg_endo) cc_final: 0.7304 (Cg_exo) REVERT: L 77 THR cc_start: 0.7380 (m) cc_final: 0.7025 (p) REVERT: O 45 THR cc_start: 0.8331 (p) cc_final: 0.8100 (p) REVERT: O 46 HIS cc_start: 0.7061 (m90) cc_final: 0.6832 (m90) REVERT: P 80 MET cc_start: 0.7002 (mmm) cc_final: 0.6618 (mmt) REVERT: Q 17 ASP cc_start: 0.7366 (p0) cc_final: 0.6756 (m-30) REVERT: R 16 MET cc_start: 0.2267 (mmm) cc_final: 0.1497 (mmm) REVERT: R 49 ILE cc_start: 0.4174 (mt) cc_final: 0.3853 (mt) REVERT: R 79 THR cc_start: 0.5497 (m) cc_final: 0.5241 (m) REVERT: T 50 TYR cc_start: 0.6643 (p90) cc_final: 0.6128 (p90) REVERT: T 60 TYR cc_start: 0.7530 (m-80) cc_final: 0.7083 (m-80) REVERT: U 75 TYR cc_start: 0.7540 (m-80) cc_final: 0.7186 (m-80) REVERT: V 46 TRP cc_start: 0.1498 (p90) cc_final: 0.0716 (p90) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.6287 time to fit residues: 394.7531 Evaluate side-chains 307 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 304 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 265 optimal weight: 0.3980 chunk 176 optimal weight: 0.0770 chunk 314 optimal weight: 0.2980 chunk 196 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 chunk 145 optimal weight: 4.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN ** C 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 GLN F 50 GLN F 64 ASN F 67 GLN J 38 HIS M 100 GLN ** O 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN ** P 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 GLN ** V 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 47053 Z= 0.145 Angle : 0.617 8.109 69749 Z= 0.321 Chirality : 0.037 0.354 8861 Planarity : 0.005 0.061 4164 Dihedral : 24.734 179.670 21890 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.54 % Favored : 97.22 % Rotamer: Outliers : 0.11 % Allowed : 1.28 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.10 (0.18), residues: 2050 helix: 0.85 (0.17), residues: 915 sheet: -0.40 (0.27), residues: 316 loop : -0.52 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 9 HIS 0.014 0.002 HIS F 118 PHE 0.019 0.002 PHE G 33 TYR 0.038 0.002 TYR S 75 ARG 0.011 0.001 ARG I 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 409 time to evaluate : 2.936 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 69 MET cc_start: 0.2952 (tmm) cc_final: 0.1947 (tmm) REVERT: C 267 LEU cc_start: 0.6393 (mt) cc_final: 0.5814 (mp) REVERT: C 399 MET cc_start: 0.0329 (tpp) cc_final: -0.0082 (tpp) REVERT: C 407 ARG cc_start: 0.4272 (ttt180) cc_final: 0.3598 (mtm180) REVERT: C 451 PHE cc_start: 0.4674 (m-10) cc_final: 0.4250 (m-10) REVERT: C 533 MET cc_start: 0.3165 (ttt) cc_final: 0.2897 (ttp) REVERT: C 560 ILE cc_start: 0.6235 (mp) cc_final: 0.6006 (mp) REVERT: C 563 TYR cc_start: 0.4921 (t80) cc_final: 0.4494 (t80) REVERT: F 77 LYS cc_start: 0.6903 (mtmt) cc_final: 0.6565 (tmmt) REVERT: F 112 GLN cc_start: 0.6535 (tm-30) cc_final: 0.6248 (tt0) REVERT: F 127 ASP cc_start: 0.8000 (p0) cc_final: 0.7558 (m-30) REVERT: F 134 LYS cc_start: 0.6505 (mmpt) cc_final: 0.6222 (mptt) REVERT: G 127 SER cc_start: 0.7049 (t) cc_final: 0.6672 (p) REVERT: G 130 SER cc_start: 0.6866 (t) cc_final: 0.6285 (t) REVERT: G 132 THR cc_start: 0.7192 (m) cc_final: 0.6723 (p) REVERT: H 59 MET cc_start: 0.5078 (mmp) cc_final: 0.4218 (ptm) REVERT: I 34 ARG cc_start: 0.8620 (mmm-85) cc_final: 0.8319 (mmt180) REVERT: I 66 TYR cc_start: 0.5746 (m-80) cc_final: 0.5104 (m-10) REVERT: J 12 ARG cc_start: 0.4520 (tpt-90) cc_final: 0.4190 (ttm170) REVERT: L 21 SER cc_start: 0.5528 (m) cc_final: 0.5078 (t) REVERT: L 55 PRO cc_start: 0.7641 (Cg_endo) cc_final: 0.7338 (Cg_exo) REVERT: L 77 THR cc_start: 0.7434 (m) cc_final: 0.7027 (p) REVERT: O 53 ARG cc_start: 0.7542 (mtp85) cc_final: 0.6426 (tpt170) REVERT: P 80 MET cc_start: 0.7038 (mmm) cc_final: 0.6622 (mmt) REVERT: Q 17 ASP cc_start: 0.7427 (p0) cc_final: 0.6900 (m-30) REVERT: Q 79 GLU cc_start: 0.7200 (tp30) cc_final: 0.6444 (pt0) REVERT: R 16 MET cc_start: 0.2873 (mmm) cc_final: 0.2635 (mmm) REVERT: R 49 ILE cc_start: 0.4016 (mt) cc_final: 0.3726 (mt) REVERT: R 79 THR cc_start: 0.5311 (m) cc_final: 0.5007 (m) REVERT: T 60 TYR cc_start: 0.7379 (m-80) cc_final: 0.6967 (m-80) REVERT: U 75 TYR cc_start: 0.7669 (m-80) cc_final: 0.7150 (m-80) REVERT: V 46 TRP cc_start: 0.1352 (p90) cc_final: 0.0321 (p90) outliers start: 2 outliers final: 0 residues processed: 410 average time/residue: 0.6213 time to fit residues: 406.1338 Evaluate side-chains 326 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 194 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 187 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 199 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 246 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 ASN M 100 GLN ** O 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.6302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 47053 Z= 0.245 Angle : 0.704 18.595 69749 Z= 0.359 Chirality : 0.041 0.371 8861 Planarity : 0.006 0.082 4164 Dihedral : 24.739 179.313 21890 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.46 % Favored : 96.34 % Rotamer: Outliers : 0.06 % Allowed : 1.45 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.18), residues: 2050 helix: 0.62 (0.16), residues: 903 sheet: -0.53 (0.27), residues: 315 loop : -0.72 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 9 HIS 0.007 0.002 HIS P 84 PHE 0.025 0.003 PHE U 18 TYR 0.031 0.002 TYR S 75 ARG 0.009 0.001 ARG L 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 375 time to evaluate : 2.714 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 69 MET cc_start: 0.2916 (tmm) cc_final: 0.2011 (tmm) REVERT: C 407 ARG cc_start: 0.4279 (ttt180) cc_final: 0.3636 (mtm180) REVERT: C 472 TYR cc_start: 0.3754 (m-10) cc_final: 0.1825 (m-80) REVERT: F 91 ASP cc_start: 0.7582 (t70) cc_final: 0.7120 (p0) REVERT: F 127 ASP cc_start: 0.7797 (p0) cc_final: 0.7430 (m-30) REVERT: F 134 LYS cc_start: 0.6602 (mmpt) cc_final: 0.6309 (mptt) REVERT: F 171 LYS cc_start: 0.6229 (ptpt) cc_final: 0.5839 (mttt) REVERT: G 48 PHE cc_start: 0.7225 (p90) cc_final: 0.6735 (m-80) REVERT: G 54 GLN cc_start: 0.5434 (tp-100) cc_final: 0.4780 (mt0) REVERT: G 127 SER cc_start: 0.7016 (t) cc_final: 0.6781 (p) REVERT: G 130 SER cc_start: 0.6867 (t) cc_final: 0.6283 (t) REVERT: G 132 THR cc_start: 0.7106 (m) cc_final: 0.6684 (p) REVERT: H 59 MET cc_start: 0.5065 (mmp) cc_final: 0.4136 (ptm) REVERT: I 34 ARG cc_start: 0.8489 (mmm-85) cc_final: 0.8067 (mmt180) REVERT: I 66 TYR cc_start: 0.5896 (m-80) cc_final: 0.5137 (m-10) REVERT: I 99 ASN cc_start: 0.7376 (t0) cc_final: 0.7064 (t0) REVERT: J 12 ARG cc_start: 0.4355 (tpt-90) cc_final: 0.4018 (ttm170) REVERT: L 21 SER cc_start: 0.5305 (m) cc_final: 0.4945 (t) REVERT: L 55 PRO cc_start: 0.7568 (Cg_endo) cc_final: 0.7261 (Cg_exo) REVERT: L 77 THR cc_start: 0.7356 (m) cc_final: 0.7026 (p) REVERT: P 10 MET cc_start: 0.7309 (ptp) cc_final: 0.6983 (ptp) REVERT: Q 17 ASP cc_start: 0.7468 (p0) cc_final: 0.6928 (m-30) REVERT: R 16 MET cc_start: 0.2732 (mmm) cc_final: 0.1986 (mmm) REVERT: R 49 ILE cc_start: 0.3827 (mt) cc_final: 0.3552 (mt) REVERT: T 46 ARG cc_start: 0.7254 (mtp85) cc_final: 0.6503 (mtp85) REVERT: T 54 ASP cc_start: 0.5136 (m-30) cc_final: 0.4485 (p0) REVERT: T 55 PHE cc_start: 0.5554 (m-80) cc_final: 0.5124 (m-80) REVERT: T 59 PHE cc_start: 0.7294 (m-80) cc_final: 0.7083 (m-80) REVERT: T 60 TYR cc_start: 0.7477 (m-80) cc_final: 0.7114 (m-80) REVERT: U 75 TYR cc_start: 0.7564 (m-80) cc_final: 0.7114 (m-80) REVERT: V 46 TRP cc_start: 0.1300 (p90) cc_final: 0.0390 (p90) outliers start: 1 outliers final: 0 residues processed: 375 average time/residue: 0.6121 time to fit residues: 371.7644 Evaluate side-chains 304 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 285 optimal weight: 1.9990 chunk 301 optimal weight: 6.9990 chunk 274 optimal weight: 5.9990 chunk 292 optimal weight: 7.9990 chunk 300 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 229 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 264 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN C 356 HIS C 462 HIS C 541 GLN ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN F 67 GLN F 112 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 ASN M 100 GLN ** O 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.6539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 47053 Z= 0.211 Angle : 0.667 10.146 69749 Z= 0.344 Chirality : 0.039 0.367 8861 Planarity : 0.005 0.062 4164 Dihedral : 24.730 179.875 21890 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.46 % Favored : 96.34 % Rotamer: Outliers : 0.17 % Allowed : 1.06 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.18), residues: 2050 helix: 0.63 (0.16), residues: 901 sheet: -0.54 (0.27), residues: 315 loop : -0.73 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP T 43 HIS 0.020 0.002 HIS C 599 PHE 0.028 0.003 PHE C 451 TYR 0.035 0.002 TYR S 75 ARG 0.009 0.001 ARG C 561 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 372 time to evaluate : 3.618 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 69 MET cc_start: 0.2980 (tmm) cc_final: 0.2105 (tmm) REVERT: C 281 TYR cc_start: 0.3066 (m-10) cc_final: 0.2402 (m-80) REVERT: C 407 ARG cc_start: 0.4262 (ttt180) cc_final: 0.3612 (mtm180) REVERT: C 563 TYR cc_start: 0.4954 (t80) cc_final: 0.4310 (t80) REVERT: F 127 ASP cc_start: 0.7740 (p0) cc_final: 0.7388 (m-30) REVERT: F 134 LYS cc_start: 0.6650 (mmpt) cc_final: 0.6348 (mptt) REVERT: G 48 PHE cc_start: 0.7152 (p90) cc_final: 0.6707 (m-80) REVERT: G 54 GLN cc_start: 0.5629 (tp-100) cc_final: 0.4876 (mt0) REVERT: G 127 SER cc_start: 0.6977 (t) cc_final: 0.6736 (p) REVERT: G 130 SER cc_start: 0.6874 (t) cc_final: 0.6283 (t) REVERT: G 132 THR cc_start: 0.7140 (m) cc_final: 0.6738 (p) REVERT: H 59 MET cc_start: 0.4994 (mmp) cc_final: 0.4054 (ptm) REVERT: I 66 TYR cc_start: 0.5961 (m-80) cc_final: 0.5288 (m-10) REVERT: J 12 ARG cc_start: 0.4419 (tpt-90) cc_final: 0.4084 (ttm170) REVERT: J 103 LEU cc_start: 0.5572 (mt) cc_final: 0.4567 (tp) REVERT: L 21 SER cc_start: 0.5337 (m) cc_final: 0.5013 (t) REVERT: L 55 PRO cc_start: 0.7515 (Cg_endo) cc_final: 0.7231 (Cg_exo) REVERT: L 77 THR cc_start: 0.7326 (m) cc_final: 0.6979 (p) REVERT: Q 17 ASP cc_start: 0.7492 (p0) cc_final: 0.6971 (m-30) REVERT: R 16 MET cc_start: 0.2799 (mmm) cc_final: 0.1875 (mmm) REVERT: R 49 ILE cc_start: 0.3982 (mt) cc_final: 0.3700 (mt) REVERT: S 32 ILE cc_start: 0.7734 (mm) cc_final: 0.7295 (pt) REVERT: S 75 TYR cc_start: 0.7375 (m-80) cc_final: 0.6741 (m-80) REVERT: T 50 TYR cc_start: 0.6230 (p90) cc_final: 0.5710 (p90) REVERT: T 54 ASP cc_start: 0.5262 (m-30) cc_final: 0.4614 (p0) REVERT: T 55 PHE cc_start: 0.5733 (m-80) cc_final: 0.5343 (m-80) REVERT: T 60 TYR cc_start: 0.7509 (m-80) cc_final: 0.7118 (m-80) REVERT: U 75 TYR cc_start: 0.7476 (m-80) cc_final: 0.7136 (m-80) REVERT: V 46 TRP cc_start: 0.1231 (p90) cc_final: 0.0306 (p90) outliers start: 3 outliers final: 0 residues processed: 373 average time/residue: 0.6105 time to fit residues: 368.3330 Evaluate side-chains 318 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 291 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 chunk 309 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 324 optimal weight: 8.9990 chunk 298 optimal weight: 4.9990 chunk 258 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 199 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN J 32 ASN M 100 GLN ** O 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 42 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.6784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 47053 Z= 0.153 Angle : 0.612 9.812 69749 Z= 0.316 Chirality : 0.037 0.374 8861 Planarity : 0.005 0.052 4164 Dihedral : 24.601 179.664 21890 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.93 % Favored : 96.83 % Rotamer: Outliers : 0.11 % Allowed : 0.45 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.08 (0.18), residues: 2050 helix: 0.87 (0.17), residues: 912 sheet: -0.27 (0.27), residues: 313 loop : -0.62 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 9 HIS 0.015 0.001 HIS C 599 PHE 0.042 0.002 PHE C 556 TYR 0.028 0.002 TYR S 75 ARG 0.011 0.001 ARG F 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 381 time to evaluate : 2.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 MET cc_start: 0.2827 (tmm) cc_final: 0.2011 (tmm) REVERT: C 267 LEU cc_start: 0.6358 (mt) cc_final: 0.6149 (mp) REVERT: C 286 HIS cc_start: 0.3087 (m-70) cc_final: 0.2739 (m90) REVERT: C 407 ARG cc_start: 0.4322 (ttt180) cc_final: 0.3694 (mtm180) REVERT: C 462 HIS cc_start: 0.7680 (t-90) cc_final: 0.7469 (t-90) REVERT: C 472 TYR cc_start: 0.3568 (m-10) cc_final: 0.1678 (m-80) REVERT: C 563 TYR cc_start: 0.4940 (t80) cc_final: 0.4507 (t80) REVERT: F 127 ASP cc_start: 0.7800 (p0) cc_final: 0.7478 (m-30) REVERT: F 134 LYS cc_start: 0.6602 (mmpt) cc_final: 0.6287 (mptt) REVERT: G 54 GLN cc_start: 0.5761 (tp-100) cc_final: 0.4913 (mt0) REVERT: G 127 SER cc_start: 0.6854 (t) cc_final: 0.6592 (p) REVERT: G 130 SER cc_start: 0.6864 (t) cc_final: 0.6365 (t) REVERT: G 132 THR cc_start: 0.7180 (m) cc_final: 0.6833 (p) REVERT: H 59 MET cc_start: 0.5034 (mmp) cc_final: 0.4068 (ptm) REVERT: I 34 ARG cc_start: 0.8599 (mmm-85) cc_final: 0.8251 (mmt180) REVERT: I 66 TYR cc_start: 0.6039 (m-80) cc_final: 0.5501 (m-10) REVERT: J 12 ARG cc_start: 0.4584 (tpt-90) cc_final: 0.4240 (ttm170) REVERT: J 103 LEU cc_start: 0.5555 (mt) cc_final: 0.4590 (tp) REVERT: L 55 PRO cc_start: 0.7618 (Cg_endo) cc_final: 0.7329 (Cg_exo) REVERT: L 87 LEU cc_start: 0.8477 (mm) cc_final: 0.7839 (tp) REVERT: O 45 THR cc_start: 0.8546 (p) cc_final: 0.8344 (p) REVERT: O 46 HIS cc_start: 0.6947 (m90) cc_final: 0.6731 (m90) REVERT: O 53 ARG cc_start: 0.7527 (mtp85) cc_final: 0.6414 (tpt170) REVERT: Q 17 ASP cc_start: 0.7461 (p0) cc_final: 0.6889 (m-30) REVERT: Q 18 LYS cc_start: 0.8145 (mttt) cc_final: 0.7560 (tptp) REVERT: Q 79 GLU cc_start: 0.7162 (tp30) cc_final: 0.6885 (tp30) REVERT: R 43 GLN cc_start: 0.5800 (mt0) cc_final: 0.4978 (mp10) REVERT: R 49 ILE cc_start: 0.3977 (mt) cc_final: 0.3709 (mt) REVERT: S 32 ILE cc_start: 0.7678 (mm) cc_final: 0.7293 (pt) REVERT: S 75 TYR cc_start: 0.7211 (m-80) cc_final: 0.6579 (m-80) REVERT: T 47 ARG cc_start: 0.6931 (mmm160) cc_final: 0.6658 (tpp-160) REVERT: T 54 ASP cc_start: 0.5282 (m-30) cc_final: 0.4708 (p0) REVERT: T 55 PHE cc_start: 0.5860 (m-80) cc_final: 0.5501 (m-80) REVERT: U 75 TYR cc_start: 0.7550 (m-80) cc_final: 0.7023 (m-80) REVERT: V 27 SER cc_start: 0.6213 (m) cc_final: 0.5530 (p) REVERT: V 46 TRP cc_start: 0.1066 (p90) cc_final: 0.0109 (p90) outliers start: 2 outliers final: 1 residues processed: 382 average time/residue: 0.6350 time to fit residues: 392.6713 Evaluate side-chains 319 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 318 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 158 optimal weight: 0.2980 chunk 205 optimal weight: 0.5980 chunk 275 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 238 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 259 optimal weight: 0.9990 chunk 108 optimal weight: 20.0000 chunk 265 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 HIS ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN J 32 ASN M 100 GLN ** O 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN ** O 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.113447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.095529 restraints weight = 184532.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.094575 restraints weight = 177874.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.095288 restraints weight = 121031.215| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 moved from start: 0.7024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 47053 Z= 0.138 Angle : 0.580 9.444 69749 Z= 0.298 Chirality : 0.035 0.379 8861 Planarity : 0.005 0.055 4164 Dihedral : 24.458 179.760 21890 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.44 % Favored : 97.37 % Rotamer: Outliers : 0.11 % Allowed : 0.28 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.18), residues: 2050 helix: 1.10 (0.17), residues: 912 sheet: -0.15 (0.27), residues: 333 loop : -0.51 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 9 HIS 0.011 0.001 HIS R 14 PHE 0.027 0.002 PHE C 451 TYR 0.036 0.002 TYR C 371 ARG 0.007 0.001 ARG C 561 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8502.87 seconds wall clock time: 159 minutes 1.50 seconds (9541.50 seconds total)