Starting phenix.real_space_refine on Fri Jul 26 04:01:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spo_40680/07_2024/8spo_40680_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spo_40680/07_2024/8spo_40680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spo_40680/07_2024/8spo_40680.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spo_40680/07_2024/8spo_40680.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spo_40680/07_2024/8spo_40680_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spo_40680/07_2024/8spo_40680_neut.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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: 6 Type Number sf(0) Gaussians P 158 5.49 5 Mg 4 5.21 5 S 85 5.16 5 C 19663 2.51 5 N 5212 2.21 5 O 6185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 186": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 31307 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3393 Classifications: {'peptide': 407} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 394} Chain breaks: 1 Chain: "B" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3787 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "C" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'RNA': 19} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "D" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 372 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "E" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3140 Classifications: {'peptide': 380} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 369} Chain breaks: 3 Chain: "F" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3787 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "G" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna3p': 20} Chain: "H" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "I" Number of atoms: 3063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3063 Classifications: {'peptide': 371} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 360} Chain breaks: 3 Chain: "J" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "K" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "L" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3787 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "M" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3265 Classifications: {'peptide': 394} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 383} Chain breaks: 2 Chain: "N" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3787 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "O" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 16} Chain: "P" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.43, per 1000 atoms: 0.59 Number of scatterers: 31307 At special positions: 0 Unit cell: (118.668, 176.204, 231.043, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 85 16.00 P 158 15.00 Mg 4 11.99 O 6185 8.00 N 5212 7.00 C 19663 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: 12.75 Conformation dependent library (CDL) restraints added in 4.8 seconds 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6522 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 42 sheets defined 36.3% alpha, 19.1% beta 33 base pairs and 117 stacking pairs defined. Time for finding SS restraints: 12.29 Creating SS restraints... Processing helix chain 'A' and resid 14 through 29 Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 71 through 88 Processing helix chain 'A' and resid 123 through 139 removed outlier: 3.883A pdb=" N GLY A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.519A pdb=" N ILE A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 257 through 280 Processing helix chain 'A' and resid 353 through 365 Processing helix chain 'A' and resid 369 through 384 removed outlier: 3.600A pdb=" N LEU A 384 " --> pdb=" O PHE A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 30 Processing helix chain 'B' and resid 46 through 60 Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 97 through 105 removed outlier: 3.618A pdb=" N ILE B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 131 removed outlier: 3.646A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 151 removed outlier: 3.655A pdb=" N TYR B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS B 151 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 201 removed outlier: 4.180A pdb=" N ASN B 201 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 215 through 218 Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.536A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 230' Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 331 through 351 Processing helix chain 'B' and resid 366 through 375 Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 478 through 490 removed outlier: 3.786A pdb=" N ALA B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'E' and resid 14 through 29 Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.819A pdb=" N GLU E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS E 51 " --> pdb=" O SER E 47 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL E 52 " --> pdb=" O ASN E 48 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE E 53 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 89 Processing helix chain 'E' and resid 109 through 114 removed outlier: 4.491A pdb=" N ARG E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 139 Processing helix chain 'E' and resid 149 through 157 removed outlier: 3.568A pdb=" N ILE E 157 " --> pdb=" O LEU E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 249 Processing helix chain 'E' and resid 257 through 280 Processing helix chain 'E' and resid 353 through 365 Processing helix chain 'E' and resid 369 through 385 removed outlier: 3.768A pdb=" N LEU E 384 " --> pdb=" O PHE E 380 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER E 385 " --> pdb=" O ILE E 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 22 through 28 removed outlier: 3.511A pdb=" N GLY F 26 " --> pdb=" O ASP F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 60 Processing helix chain 'F' and resid 77 through 83 Processing helix chain 'F' and resid 97 through 105 removed outlier: 3.825A pdb=" N ILE F 101 " --> pdb=" O THR F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 131 removed outlier: 3.679A pdb=" N LYS F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 150 removed outlier: 3.510A pdb=" N TYR F 148 " --> pdb=" O PRO F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 214 removed outlier: 3.642A pdb=" N LEU F 214 " --> pdb=" O PHE F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 230 Processing helix chain 'F' and resid 248 through 264 Processing helix chain 'F' and resid 331 through 351 Processing helix chain 'F' and resid 366 through 376 removed outlier: 3.600A pdb=" N TRP F 370 " --> pdb=" O ASN F 366 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 462 Processing helix chain 'F' and resid 477 through 480 Processing helix chain 'F' and resid 481 through 490 Processing helix chain 'F' and resid 502 through 506 removed outlier: 3.816A pdb=" N TYR F 505 " --> pdb=" O ALA F 502 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 29 Processing helix chain 'I' and resid 44 through 56 Processing helix chain 'I' and resid 71 through 89 Processing helix chain 'I' and resid 123 through 139 Processing helix chain 'I' and resid 149 through 156 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 257 through 279 Processing helix chain 'I' and resid 353 through 366 removed outlier: 3.669A pdb=" N LYS I 366 " --> pdb=" O ARG I 362 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 385 Processing helix chain 'L' and resid 15 through 17 No H-bonds generated for 'chain 'L' and resid 15 through 17' Processing helix chain 'L' and resid 22 through 30 Processing helix chain 'L' and resid 46 through 60 Processing helix chain 'L' and resid 77 through 83 Processing helix chain 'L' and resid 97 through 105 removed outlier: 3.824A pdb=" N ILE L 101 " --> pdb=" O THR L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 131 removed outlier: 4.109A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE L 125 " --> pdb=" O PHE L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 149 removed outlier: 3.685A pdb=" N TYR L 148 " --> pdb=" O PRO L 144 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 144 through 149' Processing helix chain 'L' and resid 205 through 214 removed outlier: 3.579A pdb=" N LEU L 214 " --> pdb=" O PHE L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 230 Processing helix chain 'L' and resid 248 through 264 Processing helix chain 'L' and resid 331 through 351 removed outlier: 3.591A pdb=" N ALA L 337 " --> pdb=" O LYS L 333 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU L 338 " --> pdb=" O GLU L 334 " (cutoff:3.500A) Processing helix chain 'L' and resid 366 through 371 Processing helix chain 'L' and resid 451 through 462 Processing helix chain 'L' and resid 477 through 491 removed outlier: 3.830A pdb=" N ALA L 483 " --> pdb=" O THR L 479 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP L 484 " --> pdb=" O LEU L 480 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY L 487 " --> pdb=" O ALA L 483 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR L 491 " --> pdb=" O GLY L 487 " (cutoff:3.500A) Processing helix chain 'L' and resid 502 through 506 removed outlier: 3.746A pdb=" N TYR L 505 " --> pdb=" O ALA L 502 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 27 Processing helix chain 'M' and resid 46 through 56 Processing helix chain 'M' and resid 71 through 89 Processing helix chain 'M' and resid 104 through 108 removed outlier: 3.838A pdb=" N ILE M 108 " --> pdb=" O TYR M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 113 removed outlier: 3.606A pdb=" N VAL M 113 " --> pdb=" O ILE M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 139 Processing helix chain 'M' and resid 146 through 160 removed outlier: 4.233A pdb=" N SER M 150 " --> pdb=" O ASP M 146 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE M 157 " --> pdb=" O LEU M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'M' and resid 257 through 280 Processing helix chain 'M' and resid 300 through 302 No H-bonds generated for 'chain 'M' and resid 300 through 302' Processing helix chain 'M' and resid 353 through 365 Processing helix chain 'M' and resid 366 through 368 No H-bonds generated for 'chain 'M' and resid 366 through 368' Processing helix chain 'M' and resid 369 through 384 removed outlier: 3.812A pdb=" N LEU M 384 " --> pdb=" O PHE M 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 17 No H-bonds generated for 'chain 'N' and resid 15 through 17' Processing helix chain 'N' and resid 22 through 30 Processing helix chain 'N' and resid 46 through 60 Processing helix chain 'N' and resid 77 through 83 Processing helix chain 'N' and resid 97 through 103 removed outlier: 3.671A pdb=" N LYS N 103 " --> pdb=" O GLU N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 131 removed outlier: 3.926A pdb=" N LYS N 124 " --> pdb=" O LEU N 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 151 removed outlier: 3.664A pdb=" N TYR N 148 " --> pdb=" O PRO N 144 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR N 150 " --> pdb=" O GLU N 146 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS N 151 " --> pdb=" O ILE N 147 " (cutoff:3.500A) Processing helix chain 'N' and resid 205 through 214 removed outlier: 3.575A pdb=" N LEU N 214 " --> pdb=" O PHE N 210 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 230 removed outlier: 3.500A pdb=" N ALA N 230 " --> pdb=" O GLU N 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 226 through 230' Processing helix chain 'N' and resid 248 through 264 Processing helix chain 'N' and resid 331 through 351 Processing helix chain 'N' and resid 366 through 376 removed outlier: 3.713A pdb=" N VAL N 376 " --> pdb=" O ALA N 372 " (cutoff:3.500A) Processing helix chain 'N' and resid 451 through 462 Processing helix chain 'N' and resid 463 through 465 No H-bonds generated for 'chain 'N' and resid 463 through 465' Processing helix chain 'N' and resid 481 through 490 Processing helix chain 'N' and resid 502 through 506 removed outlier: 3.680A pdb=" N TYR N 505 " --> pdb=" O ALA N 502 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.039A pdb=" N ILE A 5 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS A 4 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS A 59 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ILE A 118 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 3 removed outlier: 4.422A pdb=" N LYS A 409 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TYR A 171 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LYS A 411 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU A 169 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN A 413 " --> pdb=" O LYS A 167 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 207 through 210 removed outlier: 3.568A pdb=" N TYR A 210 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 216 " --> pdb=" O ARG A 186 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 239 " --> pdb=" O PHE A 187 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 283 through 286 removed outlier: 7.317A pdb=" N THR A 291 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLY A 325 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU A 295 " --> pdb=" O PHE A 321 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N PHE A 321 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU A 310 " --> pdb=" O PHE A 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 286 removed outlier: 7.317A pdb=" N THR A 291 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLY A 325 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU A 295 " --> pdb=" O PHE A 321 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N PHE A 321 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 324 " --> pdb=" O SER A 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 390 through 396 removed outlier: 5.931A pdb=" N GLU A 399 " --> pdb=" O MET A 395 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 6 removed outlier: 6.647A pdb=" N SER B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY B 385 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL B 357 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL B 386 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE B 359 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE B 388 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA B 361 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN B 296 " --> pdb=" O TRP B 320 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TRP B 320 " --> pdb=" O ASN B 296 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N CYS B 298 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLY B 318 " --> pdb=" O CYS B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 19 through 20 removed outlier: 3.508A pdb=" N LYS B 270 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 91 through 95 removed outlier: 6.662A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N PHE B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL B 141 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 425 through 426 removed outlier: 3.564A pdb=" N THR B 431 " --> pdb=" O VAL B 426 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 32 through 33 removed outlier: 6.036A pdb=" N PHE E 6 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL E 63 " --> pdb=" O PHE E 6 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N SER E 8 " --> pdb=" O VAL E 63 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 2 through 3 Processing sheet with id=AB4, first strand: chain 'E' and resid 283 through 286 removed outlier: 7.445A pdb=" N THR E 291 " --> pdb=" O GLY E 325 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLY E 325 " --> pdb=" O THR E 291 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 283 through 286 removed outlier: 7.445A pdb=" N THR E 291 " --> pdb=" O GLY E 325 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLY E 325 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU E 176 " --> pdb=" O LEU E 335 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N SER E 177 " --> pdb=" O SER E 404 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE E 402 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 208 through 210 removed outlier: 3.575A pdb=" N TYR E 210 " --> pdb=" O TYR E 213 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 304 through 305 Processing sheet with id=AB8, first strand: chain 'F' and resid 5 through 6 removed outlier: 6.631A pdb=" N SER F 417 " --> pdb=" O VAL F 413 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLY F 385 " --> pdb=" O ASN F 446 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL F 278 " --> pdb=" O LEU F 305 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU F 305 " --> pdb=" O VAL F 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 19 through 20 Processing sheet with id=AC1, first strand: chain 'F' and resid 93 through 95 removed outlier: 8.461A pdb=" N LYS F 94 " --> pdb=" O SER F 41 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL F 43 " --> pdb=" O LYS F 94 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY F 42 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE F 142 " --> pdb=" O GLY F 42 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE F 44 " --> pdb=" O ILE F 142 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 284 through 286 removed outlier: 3.706A pdb=" N VAL F 284 " --> pdb=" O CYS F 299 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 425 through 426 removed outlier: 3.609A pdb=" N THR F 431 " --> pdb=" O VAL F 426 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 32 through 33 removed outlier: 6.411A pdb=" N ILE I 5 " --> pdb=" O TRP I 33 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE I 6 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL I 63 " --> pdb=" O PHE I 6 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER I 8 " --> pdb=" O VAL I 63 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 2 through 3 Processing sheet with id=AC6, first strand: chain 'I' and resid 311 through 314 removed outlier: 3.563A pdb=" N TRP I 319 " --> pdb=" O GLY I 312 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N SER I 177 " --> pdb=" O SER I 404 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE I 402 " --> pdb=" O LEU I 179 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 208 through 210 removed outlier: 3.581A pdb=" N TYR I 210 " --> pdb=" O TYR I 213 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 283 through 286 Processing sheet with id=AC9, first strand: chain 'L' and resid 5 through 6 removed outlier: 6.527A pdb=" N GLY L 385 " --> pdb=" O ASN L 446 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL L 357 " --> pdb=" O VAL L 384 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL L 386 " --> pdb=" O VAL L 357 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE L 359 " --> pdb=" O VAL L 386 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE L 388 " --> pdb=" O ILE L 359 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ALA L 361 " --> pdb=" O ILE L 388 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL L 278 " --> pdb=" O LEU L 305 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU L 305 " --> pdb=" O VAL L 278 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS L 286 " --> pdb=" O ALA L 297 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG L 295 " --> pdb=" O VAL L 288 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE L 304 " --> pdb=" O VAL L 312 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY L 310 " --> pdb=" O ASP L 306 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 19 through 20 Processing sheet with id=AD2, first strand: chain 'L' and resid 91 through 95 removed outlier: 7.003A pdb=" N SER L 41 " --> pdb=" O THR L 92 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LYS L 94 " --> pdb=" O SER L 41 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL L 43 " --> pdb=" O LYS L 94 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY L 42 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE L 142 " --> pdb=" O GLY L 42 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE L 44 " --> pdb=" O ILE L 142 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TRP L 139 " --> pdb=" O GLN L 222 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N PHE L 224 " --> pdb=" O TRP L 139 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL L 141 " --> pdb=" O PHE L 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'L' and resid 425 through 426 Processing sheet with id=AD4, first strand: chain 'M' and resid 31 through 33 removed outlier: 6.934A pdb=" N LYS M 4 " --> pdb=" O LYS M 59 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N LEU M 61 " --> pdb=" O LYS M 4 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE M 6 " --> pdb=" O LEU M 61 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL M 63 " --> pdb=" O PHE M 6 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N SER M 8 " --> pdb=" O VAL M 63 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N PHE M 60 " --> pdb=" O ILE M 95 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU M 97 " --> pdb=" O PHE M 60 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU M 62 " --> pdb=" O LEU M 97 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 2 through 3 removed outlier: 7.661A pdb=" N LYS M 409 " --> pdb=" O LYS N 2 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL M 414 " --> pdb=" O LYS M 167 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LYS M 167 " --> pdb=" O VAL M 414 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 178 through 180 removed outlier: 6.300A pdb=" N PHE M 402 " --> pdb=" O LEU M 179 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 187 through 188 Processing sheet with id=AD8, first strand: chain 'M' and resid 283 through 286 Processing sheet with id=AD9, first strand: chain 'M' and resid 304 through 305 Processing sheet with id=AE1, first strand: chain 'M' and resid 311 through 314 removed outlier: 3.589A pdb=" N SER M 324 " --> pdb=" O SER M 338 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS M 328 " --> pdb=" O VAL M 334 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 5 through 6 removed outlier: 6.812A pdb=" N GLY N 385 " --> pdb=" O ASN N 446 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL N 357 " --> pdb=" O VAL N 384 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL N 386 " --> pdb=" O VAL N 357 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE N 359 " --> pdb=" O VAL N 386 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE N 388 " --> pdb=" O ILE N 359 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA N 361 " --> pdb=" O ILE N 388 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N CYS N 279 " --> pdb=" O PHE N 358 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N HIS N 360 " --> pdb=" O CYS N 279 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU N 281 " --> pdb=" O HIS N 360 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 5 through 6 removed outlier: 6.812A pdb=" N GLY N 385 " --> pdb=" O ASN N 446 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL N 357 " --> pdb=" O VAL N 384 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL N 386 " --> pdb=" O VAL N 357 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE N 359 " --> pdb=" O VAL N 386 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE N 388 " --> pdb=" O ILE N 359 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA N 361 " --> pdb=" O ILE N 388 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N CYS N 279 " --> pdb=" O PHE N 358 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N HIS N 360 " --> pdb=" O CYS N 279 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU N 281 " --> pdb=" O HIS N 360 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 19 through 20 Processing sheet with id=AE5, first strand: chain 'N' and resid 92 through 95 removed outlier: 6.361A pdb=" N GLY N 42 " --> pdb=" O PHE N 140 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE N 142 " --> pdb=" O GLY N 42 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE N 44 " --> pdb=" O ILE N 142 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP N 139 " --> pdb=" O GLN N 222 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N PHE N 224 " --> pdb=" O TRP N 139 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL N 141 " --> pdb=" O PHE N 224 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 425 through 426 1145 hydrogen bonds defined for protein. 3222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 166 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 117 stacking parallelities Total time for adding SS restraints: 12.32 Time building geometry restraints manager: 13.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6587 1.33 - 1.45: 8124 1.45 - 1.57: 17225 1.57 - 1.69: 308 1.69 - 1.81: 126 Bond restraints: 32370 Sorted by residual: bond pdb=" C SER N 109 " pdb=" N THR N 110 " ideal model delta sigma weight residual 1.335 1.247 0.088 1.31e-02 5.83e+03 4.48e+01 bond pdb=" C ASP N 137 " pdb=" N VAL N 138 " ideal model delta sigma weight residual 1.332 1.268 0.064 1.37e-02 5.33e+03 2.20e+01 bond pdb=" C ILE N 91 " pdb=" N THR N 92 " ideal model delta sigma weight residual 1.331 1.276 0.055 1.38e-02 5.25e+03 1.58e+01 bond pdb=" C TYR A 154 " pdb=" O TYR A 154 " ideal model delta sigma weight residual 1.236 1.281 -0.045 1.15e-02 7.56e+03 1.51e+01 bond pdb=" C GLY L 90 " pdb=" N ILE L 91 " ideal model delta sigma weight residual 1.329 1.391 -0.062 1.69e-02 3.50e+03 1.33e+01 ... (remaining 32365 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.46: 1589 106.46 - 113.56: 17693 113.56 - 120.66: 13724 120.66 - 127.76: 10919 127.76 - 134.87: 524 Bond angle restraints: 44449 Sorted by residual: angle pdb=" N ASN E 48 " pdb=" CA ASN E 48 " pdb=" C ASN E 48 " ideal model delta sigma weight residual 113.72 104.86 8.86 1.30e+00 5.92e-01 4.64e+01 angle pdb=" C ASN E 48 " pdb=" CA ASN E 48 " pdb=" CB ASN E 48 " ideal model delta sigma weight residual 109.55 118.58 -9.03 1.68e+00 3.54e-01 2.89e+01 angle pdb=" N SER A 148 " pdb=" CA SER A 148 " pdb=" C SER A 148 " ideal model delta sigma weight residual 111.28 105.58 5.70 1.09e+00 8.42e-01 2.74e+01 angle pdb=" CA ILE E 157 " pdb=" C ILE E 157 " pdb=" O ILE E 157 " ideal model delta sigma weight residual 121.98 115.83 6.15 1.21e+00 6.83e-01 2.59e+01 angle pdb=" C VAL M 164 " pdb=" N ILE M 165 " pdb=" CA ILE M 165 " ideal model delta sigma weight residual 123.19 117.09 6.10 1.24e+00 6.50e-01 2.42e+01 ... (remaining 44444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 18641 35.93 - 71.85: 616 71.85 - 107.78: 44 107.78 - 143.70: 9 143.70 - 179.63: 32 Dihedral angle restraints: 19342 sinusoidal: 9256 harmonic: 10086 Sorted by residual: dihedral pdb=" O4' U J 17 " pdb=" C1' U J 17 " pdb=" N1 U J 17 " pdb=" C2 U J 17 " ideal model delta sinusoidal sigma weight residual -160.00 19.63 -179.63 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U O 17 " pdb=" C1' U O 17 " pdb=" N1 U O 17 " pdb=" C2 U O 17 " ideal model delta sinusoidal sigma weight residual -160.00 19.61 -179.61 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U G 13 " pdb=" C1' U G 13 " pdb=" N1 U G 13 " pdb=" C2 U G 13 " ideal model delta sinusoidal sigma weight residual -160.00 16.40 -176.40 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 19339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.105: 4889 1.105 - 2.210: 0 2.210 - 3.315: 0 3.315 - 4.421: 0 4.421 - 5.526: 12 Chirality restraints: 4901 Sorted by residual: chirality pdb=" C3D NAD E 501 " pdb=" C2D NAD E 501 " pdb=" C4D NAD E 501 " pdb=" O3D NAD E 501 " both_signs ideal model delta sigma weight residual False -2.73 2.80 -5.53 2.00e-01 2.50e+01 7.63e+02 chirality pdb=" C3D NAD I 501 " pdb=" C2D NAD I 501 " pdb=" C4D NAD I 501 " pdb=" O3D NAD I 501 " both_signs ideal model delta sigma weight residual False -2.73 2.79 -5.51 2.00e-01 2.50e+01 7.60e+02 chirality pdb=" C3B NAD E 501 " pdb=" C2B NAD E 501 " pdb=" C4B NAD E 501 " pdb=" O3B NAD E 501 " both_signs ideal model delta sigma weight residual False -2.71 2.71 -5.42 2.00e-01 2.50e+01 7.35e+02 ... (remaining 4898 not shown) Planarity restraints: 5060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 146 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C ASP A 146 " -0.063 2.00e-02 2.50e+03 pdb=" O ASP A 146 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA A 147 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR M 154 " -0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C TYR M 154 " 0.057 2.00e-02 2.50e+03 pdb=" O TYR M 154 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN M 155 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 105 " -0.033 2.00e-02 2.50e+03 1.97e-02 7.78e+00 pdb=" CG TYR A 105 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 105 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 105 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 105 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 105 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 105 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 105 " -0.009 2.00e-02 2.50e+03 ... (remaining 5057 not shown) Histogram of nonbonded interaction distances: 0.33 - 1.25: 37 1.25 - 2.16: 200 2.16 - 3.07: 20662 3.07 - 3.99: 79333 3.99 - 4.90: 151707 Warning: very small nonbonded interaction distances. Nonbonded interactions: 251939 Sorted by model distance: nonbonded pdb=" CD LYS B 504 " pdb=" CA ASP F 133 " model vdw 0.334 3.870 nonbonded pdb=" NZ LYS B 504 " pdb=" N GLU F 134 " model vdw 0.498 3.200 nonbonded pdb=" N ASP B 133 " pdb=" NZ LYS F 504 " model vdw 0.527 3.200 nonbonded pdb=" C ASP L 133 " pdb=" CE LYS N 504 " model vdw 0.589 3.670 nonbonded pdb=" CB LYS B 504 " pdb=" OD1 ASP F 133 " model vdw 0.663 3.440 ... (remaining 251934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 156 or resid 169 through 186 or resid 200 throug \ h 216 or resid 241 through 420)) selection = (chain 'E' and (resid 2 through 156 or resid 169 through 238 or resid 241 throug \ h 296 or resid 309 through 420)) selection = (chain 'I' and (resid 2 through 216 or resid 241 through 296 or resid 309 throug \ h 420)) selection = (chain 'M' and (resid 2 through 156 or resid 169 through 186 or resid 200 throug \ h 216 or resid 241 through 296 or resid 309 through 420)) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 1 through 19) selection = (chain 'J' and resid 1 through 19) selection = chain 'O' } ncs_group { reference = (chain 'D' and resid 8 through 23) selection = (chain 'H' and resid 8 through 23) selection = (chain 'K' and resid 8 through 23) selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.000 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: 1.340 Check model and map are aligned: 0.250 Set scattering table: 0.290 Process input model: 93.040 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.150 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:14.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2871 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 : 0.004 0.088 32370 Z= 0.229 Angle : 0.597 9.028 44449 Z= 0.351 Chirality : 0.258 5.526 4901 Planarity : 0.004 0.087 5060 Dihedral : 18.839 179.631 12820 Min Nonbonded Distance : 0.334 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 3386 helix: 1.00 (0.16), residues: 1111 sheet: -0.99 (0.19), residues: 704 loop : -1.99 (0.14), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 33 HIS 0.006 0.001 HIS M 188 PHE 0.015 0.001 PHE F 14 TYR 0.044 0.001 TYR A 105 ARG 0.003 0.000 ARG F 407 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 3.019 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: A 157 ILE cc_start: 0.6983 (mt) cc_final: 0.6556 (mt) REVERT: A 277 MET cc_start: -0.0343 (mmm) cc_final: -0.1430 (mmm) REVERT: B 307 ASN cc_start: 0.6718 (p0) cc_final: 0.6435 (p0) REVERT: B 345 SER cc_start: 0.4870 (t) cc_final: 0.4639 (m) REVERT: F 490 LEU cc_start: 0.6896 (pp) cc_final: 0.6693 (pp) REVERT: L 280 TYR cc_start: 0.1927 (m-80) cc_final: 0.1375 (m-80) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 1.1809 time to fit residues: 441.9675 Evaluate side-chains 249 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 295 optimal weight: 40.0000 chunk 265 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 274 optimal weight: 0.4980 chunk 106 optimal weight: 4.9990 chunk 166 optimal weight: 0.4980 chunk 204 optimal weight: 8.9990 chunk 317 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 HIS B 296 ASN B 446 ASN F 16 HIS F 18 GLN L 327 GLN L 349 GLN ** L 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 ASN ** N 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 329 HIS ** N 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 446 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3513 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 32370 Z= 0.295 Angle : 0.758 16.596 44449 Z= 0.395 Chirality : 0.048 0.321 4901 Planarity : 0.005 0.058 5060 Dihedral : 18.722 179.097 5854 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.67 % Allowed : 7.19 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.12 (0.14), residues: 3386 helix: 0.89 (0.16), residues: 1130 sheet: -0.65 (0.20), residues: 659 loop : -2.05 (0.14), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP N 139 HIS 0.009 0.001 HIS B 360 PHE 0.029 0.002 PHE F 503 TYR 0.031 0.002 TYR N 65 ARG 0.013 0.001 ARG L 481 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 270 time to evaluate : 3.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.3675 (OUTLIER) cc_final: 0.2911 (mtmt) REVERT: A 277 MET cc_start: -0.0625 (mmm) cc_final: -0.1466 (mmm) REVERT: B 412 VAL cc_start: 0.3897 (OUTLIER) cc_final: 0.2748 (m) REVERT: F 1 MET cc_start: 0.2200 (mmm) cc_final: 0.1903 (mmm) REVERT: F 14 PHE cc_start: 0.5283 (m-80) cc_final: 0.4648 (m-80) REVERT: F 223 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6880 (mm) REVERT: I 35 ASP cc_start: 0.6405 (OUTLIER) cc_final: 0.5831 (t70) REVERT: I 277 MET cc_start: 0.4081 (tpp) cc_final: 0.3764 (mmm) REVERT: N 381 THR cc_start: 0.7498 (p) cc_final: 0.7288 (p) outliers start: 51 outliers final: 18 residues processed: 298 average time/residue: 1.1373 time to fit residues: 415.7926 Evaluate side-chains 257 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 235 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain L residue 219 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 256 ILE Chi-restraints excluded: chain N residue 495 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 176 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 264 optimal weight: 0.9980 chunk 216 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 318 optimal weight: 0.9990 chunk 343 optimal weight: 0.7980 chunk 283 optimal weight: 6.9990 chunk 315 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 255 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 156 GLN A 314 GLN A 358 HIS B 66 ASN B 129 ASN B 360 HIS B 430 GLN F 34 ASN F 66 ASN F 205 GLN F 414 ASN ** L 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 358 HIS N 129 ASN N 135 ASN N 360 HIS ** N 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3717 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32370 Z= 0.256 Angle : 0.652 18.143 44449 Z= 0.345 Chirality : 0.044 0.225 4901 Planarity : 0.005 0.057 5060 Dihedral : 18.491 179.594 5854 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.45 % Allowed : 9.80 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.96 (0.14), residues: 3386 helix: 1.00 (0.16), residues: 1136 sheet: -0.65 (0.21), residues: 648 loop : -1.89 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 20 HIS 0.007 0.001 HIS L 217 PHE 0.031 0.002 PHE I 120 TYR 0.020 0.002 TYR M 210 ARG 0.006 0.000 ARG L 481 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 255 time to evaluate : 3.680 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: A 277 MET cc_start: -0.0550 (mmm) cc_final: -0.1273 (mmm) REVERT: F 1 MET cc_start: 0.2692 (mmm) cc_final: 0.2302 (mmm) REVERT: F 14 PHE cc_start: 0.5502 (m-80) cc_final: 0.4476 (m-80) REVERT: F 134 GLU cc_start: 0.3601 (mp0) cc_final: 0.3198 (tt0) REVERT: F 223 ILE cc_start: 0.7122 (OUTLIER) cc_final: 0.6795 (mm) REVERT: I 277 MET cc_start: 0.3934 (tpp) cc_final: 0.3601 (mmm) REVERT: N 25 ASP cc_start: 0.5832 (m-30) cc_final: 0.5613 (m-30) outliers start: 75 outliers final: 32 residues processed: 305 average time/residue: 1.0470 time to fit residues: 400.4931 Evaluate side-chains 264 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 231 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 463 THR Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 40 ASP Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 327 SER Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 489 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 429 ILE Chi-restraints excluded: chain N residue 495 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 314 optimal weight: 2.9990 chunk 239 optimal weight: 0.0470 chunk 165 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 151 optimal weight: 0.7980 chunk 213 optimal weight: 5.9990 chunk 319 optimal weight: 0.8980 chunk 338 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 302 optimal weight: 0.0870 chunk 91 optimal weight: 0.8980 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 364 GLN ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 358 HIS N 66 ASN N 205 GLN ** N 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3712 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 32370 Z= 0.191 Angle : 0.589 16.688 44449 Z= 0.308 Chirality : 0.042 0.193 4901 Planarity : 0.004 0.054 5060 Dihedral : 18.368 179.864 5854 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.38 % Allowed : 11.79 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.71 (0.14), residues: 3386 helix: 1.29 (0.16), residues: 1135 sheet: -0.44 (0.21), residues: 627 loop : -1.84 (0.14), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 20 HIS 0.010 0.001 HIS B 329 PHE 0.026 0.002 PHE I 120 TYR 0.021 0.001 TYR M 210 ARG 0.005 0.000 ARG L 481 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 239 time to evaluate : 3.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: 0.0172 (mmm) cc_final: -0.1476 (mmm) REVERT: A 378 LEU cc_start: 0.1188 (OUTLIER) cc_final: 0.0919 (tp) REVERT: B 356 GLU cc_start: 0.5192 (tm-30) cc_final: 0.4705 (tm-30) REVERT: F 1 MET cc_start: 0.2667 (mmm) cc_final: 0.2294 (mmm) REVERT: F 14 PHE cc_start: 0.5455 (m-80) cc_final: 0.4395 (m-80) REVERT: F 33 LEU cc_start: 0.7144 (tt) cc_final: 0.6906 (tt) REVERT: F 223 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6781 (mm) REVERT: F 283 LEU cc_start: 0.4849 (OUTLIER) cc_final: 0.4540 (tp) REVERT: I 277 MET cc_start: 0.3882 (tpp) cc_final: 0.3605 (mmm) REVERT: I 336 MET cc_start: 0.4218 (mpt) cc_final: 0.3873 (mpt) REVERT: L 1 MET cc_start: 0.4544 (tpp) cc_final: 0.4267 (tpp) REVERT: M 370 ASN cc_start: 0.1279 (OUTLIER) cc_final: 0.0712 (t0) REVERT: M 395 MET cc_start: 0.2299 (ppp) cc_final: -0.0540 (pmm) REVERT: N 19 LYS cc_start: 0.7103 (ttmm) cc_final: 0.6558 (mmtp) REVERT: N 443 ILE cc_start: 0.0319 (OUTLIER) cc_final: -0.0605 (mt) outliers start: 73 outliers final: 34 residues processed: 290 average time/residue: 1.0592 time to fit residues: 382.5779 Evaluate side-chains 263 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 224 time to evaluate : 3.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 463 THR Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 327 SER Chi-restraints excluded: chain L residue 447 LYS Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 161 ASP Chi-restraints excluded: chain M residue 254 ASN Chi-restraints excluded: chain M residue 370 ASN Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain N residue 429 ILE Chi-restraints excluded: chain N residue 443 ILE Chi-restraints excluded: chain N residue 490 LEU Chi-restraints excluded: chain N residue 495 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 281 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 chunk 4 optimal weight: 0.0170 chunk 251 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 288 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 303 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 HIS ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN E 405 ASN ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 HIS M 358 HIS ** N 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 446 ASN N 454 GLN ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3897 moved from start: 0.6004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 32370 Z= 0.260 Angle : 0.664 23.147 44449 Z= 0.346 Chirality : 0.044 0.222 4901 Planarity : 0.005 0.058 5060 Dihedral : 18.480 178.393 5854 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.68 % Allowed : 13.03 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.98 (0.14), residues: 3386 helix: 1.01 (0.16), residues: 1132 sheet: -0.61 (0.21), residues: 626 loop : -1.93 (0.14), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.002 TRP A 20 HIS 0.006 0.001 HIS L 217 PHE 0.031 0.002 PHE I 120 TYR 0.023 0.002 TYR M 210 ARG 0.007 0.001 ARG L 481 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 249 time to evaluate : 2.999 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: A 277 MET cc_start: -0.0216 (mmm) cc_final: -0.1766 (mmm) REVERT: A 378 LEU cc_start: 0.1216 (OUTLIER) cc_final: 0.0914 (tp) REVERT: B 132 GLU cc_start: 0.5366 (OUTLIER) cc_final: 0.5100 (mt-10) REVERT: B 356 GLU cc_start: 0.4977 (tm-30) cc_final: 0.4571 (tm-30) REVERT: B 370 TRP cc_start: 0.3405 (t-100) cc_final: 0.3027 (t-100) REVERT: E 121 LYS cc_start: 0.6883 (OUTLIER) cc_final: 0.6652 (mtmm) REVERT: F 1 MET cc_start: 0.2647 (mmm) cc_final: 0.2213 (mmm) REVERT: F 14 PHE cc_start: 0.5623 (m-80) cc_final: 0.4363 (m-80) REVERT: F 33 LEU cc_start: 0.7183 (tt) cc_final: 0.6971 (tt) REVERT: F 223 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6745 (mm) REVERT: F 283 LEU cc_start: 0.4617 (OUTLIER) cc_final: 0.4357 (tp) REVERT: I 135 PHE cc_start: 0.5710 (m-10) cc_final: 0.5312 (m-10) REVERT: I 277 MET cc_start: 0.3841 (tpp) cc_final: 0.3596 (mmm) REVERT: I 336 MET cc_start: 0.4165 (mpt) cc_final: 0.3903 (mpt) REVERT: L 1 MET cc_start: 0.4590 (tpp) cc_final: 0.4373 (tpp) REVERT: L 14 PHE cc_start: 0.5385 (m-80) cc_final: 0.4990 (m-80) REVERT: M 15 ASN cc_start: 0.1780 (OUTLIER) cc_final: 0.1256 (m-40) REVERT: N 443 ILE cc_start: 0.0895 (OUTLIER) cc_final: -0.0056 (mt) outliers start: 82 outliers final: 43 residues processed: 313 average time/residue: 1.0812 time to fit residues: 421.1016 Evaluate side-chains 279 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 229 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 463 THR Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 327 SER Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain L residue 435 MET Chi-restraints excluded: chain L residue 447 LYS Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 494 THR Chi-restraints excluded: chain M residue 15 ASN Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 185 LEU Chi-restraints excluded: chain M residue 370 ASN Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 256 ILE Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain N residue 443 ILE Chi-restraints excluded: chain N residue 495 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 113 optimal weight: 0.5980 chunk 304 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 83 optimal weight: 0.0040 chunk 338 optimal weight: 2.9990 chunk 281 optimal weight: 10.0000 chunk 156 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 177 optimal weight: 0.9980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 364 GLN E 405 ASN F 135 ASN ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN M 358 HIS N 217 HIS ** N 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3862 moved from start: 0.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32370 Z= 0.202 Angle : 0.604 20.233 44449 Z= 0.312 Chirality : 0.042 0.322 4901 Planarity : 0.004 0.055 5060 Dihedral : 18.353 179.732 5854 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.65 % Allowed : 13.82 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.85 (0.14), residues: 3386 helix: 1.15 (0.16), residues: 1139 sheet: -0.48 (0.21), residues: 620 loop : -1.91 (0.14), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP A 20 HIS 0.005 0.001 HIS L 207 PHE 0.032 0.002 PHE F 261 TYR 0.021 0.001 TYR M 210 ARG 0.004 0.000 ARG L 364 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 236 time to evaluate : 2.855 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: A 277 MET cc_start: -0.0185 (mmm) cc_final: -0.1751 (mmm) REVERT: B 132 GLU cc_start: 0.5171 (OUTLIER) cc_final: 0.4922 (mt-10) REVERT: B 356 GLU cc_start: 0.5038 (tm-30) cc_final: 0.4709 (tm-30) REVERT: B 370 TRP cc_start: 0.3212 (t-100) cc_final: 0.1992 (t-100) REVERT: E 35 ASP cc_start: 0.4287 (OUTLIER) cc_final: 0.3800 (OUTLIER) REVERT: F 1 MET cc_start: 0.2670 (mmm) cc_final: 0.2203 (mmm) REVERT: F 14 PHE cc_start: 0.5509 (m-80) cc_final: 0.4302 (m-80) REVERT: F 223 ILE cc_start: 0.6934 (OUTLIER) cc_final: 0.6662 (mm) REVERT: F 283 LEU cc_start: 0.4556 (OUTLIER) cc_final: 0.4323 (tp) REVERT: I 135 PHE cc_start: 0.5702 (m-10) cc_final: 0.5352 (m-10) REVERT: I 277 MET cc_start: 0.3676 (tpp) cc_final: 0.3423 (mmm) REVERT: I 336 MET cc_start: 0.4253 (mpt) cc_final: 0.3964 (mpt) REVERT: I 370 ASN cc_start: 0.5025 (OUTLIER) cc_final: 0.4680 (t0) REVERT: I 395 MET cc_start: 0.3243 (OUTLIER) cc_final: 0.2918 (ppp) REVERT: L 139 TRP cc_start: 0.5943 (m100) cc_final: 0.4979 (t-100) REVERT: M 15 ASN cc_start: 0.1646 (OUTLIER) cc_final: 0.1192 (m-40) REVERT: M 370 ASN cc_start: 0.1893 (OUTLIER) cc_final: 0.1599 (p0) REVERT: N 19 LYS cc_start: 0.7029 (ttmm) cc_final: 0.6511 (mmtp) REVERT: N 24 ARG cc_start: 0.6266 (mpp80) cc_final: 0.5958 (mtm180) REVERT: N 370 TRP cc_start: 0.2846 (t-100) cc_final: 0.2498 (t-100) REVERT: N 443 ILE cc_start: 0.0917 (OUTLIER) cc_final: 0.0099 (mt) outliers start: 81 outliers final: 47 residues processed: 298 average time/residue: 1.0673 time to fit residues: 397.9390 Evaluate side-chains 280 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 225 time to evaluate : 3.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 407 ARG Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 463 THR Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 327 SER Chi-restraints excluded: chain I residue 370 ASN Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain L residue 447 LYS Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain M residue 15 ASN Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 161 ASP Chi-restraints excluded: chain M residue 265 ILE Chi-restraints excluded: chain M residue 370 ASN Chi-restraints excluded: chain N residue 256 ILE Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain N residue 429 ILE Chi-restraints excluded: chain N residue 443 ILE Chi-restraints excluded: chain N residue 463 THR Chi-restraints excluded: chain N residue 490 LEU Chi-restraints excluded: chain N residue 495 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 326 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 247 optimal weight: 6.9990 chunk 191 optimal weight: 8.9990 chunk 285 optimal weight: 5.9990 chunk 189 optimal weight: 0.0020 chunk 337 optimal weight: 0.6980 chunk 211 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 ASN B 217 HIS B 341 GLN ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 ASN ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 358 HIS N 430 GLN ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4014 moved from start: 0.7087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 32370 Z= 0.298 Angle : 0.701 26.016 44449 Z= 0.363 Chirality : 0.045 0.224 4901 Planarity : 0.005 0.057 5060 Dihedral : 18.459 178.853 5854 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.04 % Allowed : 14.60 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.17 (0.14), residues: 3386 helix: 0.78 (0.16), residues: 1124 sheet: -0.44 (0.21), residues: 589 loop : -2.06 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 20 HIS 0.008 0.001 HIS A 188 PHE 0.029 0.002 PHE I 45 TYR 0.023 0.002 TYR M 210 ARG 0.006 0.001 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 244 time to evaluate : 3.046 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: A 174 ASN cc_start: 0.1722 (OUTLIER) cc_final: 0.1476 (p0) REVERT: A 277 MET cc_start: -0.0149 (mmm) cc_final: -0.1732 (mmm) REVERT: A 378 LEU cc_start: 0.1190 (OUTLIER) cc_final: 0.0989 (tp) REVERT: B 370 TRP cc_start: 0.3977 (t-100) cc_final: 0.2583 (t-100) REVERT: F 1 MET cc_start: 0.2692 (mmm) cc_final: 0.2139 (mmm) REVERT: F 136 VAL cc_start: 0.2766 (OUTLIER) cc_final: 0.2387 (t) REVERT: F 223 ILE cc_start: 0.6871 (OUTLIER) cc_final: 0.6643 (mm) REVERT: F 283 LEU cc_start: 0.4728 (OUTLIER) cc_final: 0.4402 (tp) REVERT: I 135 PHE cc_start: 0.5759 (m-10) cc_final: 0.5426 (m-10) REVERT: I 336 MET cc_start: 0.4507 (mpt) cc_final: 0.4199 (mpt) REVERT: I 370 ASN cc_start: 0.5087 (OUTLIER) cc_final: 0.4844 (t0) REVERT: M 15 ASN cc_start: 0.1779 (OUTLIER) cc_final: 0.1301 (m-40) REVERT: M 370 ASN cc_start: 0.2550 (OUTLIER) cc_final: 0.1761 (t0) REVERT: M 395 MET cc_start: 0.1129 (ppp) cc_final: 0.0631 (ppp) REVERT: N 19 LYS cc_start: 0.7083 (ttmm) cc_final: 0.6826 (ttmm) REVERT: N 24 ARG cc_start: 0.6285 (mpp80) cc_final: 0.5879 (mtt-85) REVERT: N 106 TYR cc_start: -0.0018 (OUTLIER) cc_final: -0.1461 (m-80) REVERT: N 370 TRP cc_start: 0.3003 (t-100) cc_final: 0.2649 (t-100) REVERT: N 443 ILE cc_start: 0.1195 (OUTLIER) cc_final: 0.0372 (mt) outliers start: 93 outliers final: 53 residues processed: 311 average time/residue: 1.0204 time to fit residues: 397.1127 Evaluate side-chains 298 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 235 time to evaluate : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 407 ARG Chi-restraints excluded: chain F residue 414 ASN Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 463 THR Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 46 TRP Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 370 ASN Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 435 MET Chi-restraints excluded: chain L residue 447 LYS Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain M residue 15 ASN Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 370 ASN Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain N residue 106 TYR Chi-restraints excluded: chain N residue 256 ILE Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain N residue 429 ILE Chi-restraints excluded: chain N residue 443 ILE Chi-restraints excluded: chain N residue 495 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 208 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 chunk 201 optimal weight: 0.3980 chunk 101 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 0.0970 chunk 214 optimal weight: 3.9990 chunk 229 optimal weight: 0.3980 chunk 166 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 265 optimal weight: 1.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 ASN I 254 ASN ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3894 moved from start: 0.7147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32370 Z= 0.180 Angle : 0.604 19.586 44449 Z= 0.311 Chirality : 0.042 0.428 4901 Planarity : 0.004 0.052 5060 Dihedral : 18.271 179.866 5854 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.16 % Allowed : 16.07 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.90 (0.14), residues: 3386 helix: 1.09 (0.16), residues: 1128 sheet: -0.40 (0.22), residues: 567 loop : -1.93 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP I 20 HIS 0.004 0.001 HIS L 207 PHE 0.024 0.001 PHE I 45 TYR 0.021 0.001 TYR M 210 ARG 0.006 0.000 ARG I 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 227 time to evaluate : 3.174 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: A 277 MET cc_start: -0.0101 (mmm) cc_final: -0.1678 (mmm) REVERT: A 378 LEU cc_start: 0.1276 (OUTLIER) cc_final: 0.1056 (tp) REVERT: B 132 GLU cc_start: 0.5138 (OUTLIER) cc_final: 0.4929 (mt-10) REVERT: B 370 TRP cc_start: 0.3669 (t-100) cc_final: 0.2508 (t-100) REVERT: E 6 PHE cc_start: 0.5494 (t80) cc_final: 0.3858 (t80) REVERT: E 35 ASP cc_start: 0.4215 (OUTLIER) cc_final: 0.3965 (p0) REVERT: E 99 ILE cc_start: 0.4657 (pt) cc_final: 0.4438 (pt) REVERT: F 1 MET cc_start: 0.2618 (mmm) cc_final: 0.2059 (mmm) REVERT: F 14 PHE cc_start: 0.5563 (m-80) cc_final: 0.4196 (m-80) REVERT: F 223 ILE cc_start: 0.6782 (OUTLIER) cc_final: 0.6520 (mm) REVERT: I 336 MET cc_start: 0.4215 (mpt) cc_final: 0.3933 (mpt) REVERT: I 370 ASN cc_start: 0.4856 (OUTLIER) cc_final: 0.4633 (t0) REVERT: I 395 MET cc_start: 0.3787 (OUTLIER) cc_final: 0.3339 (pp-130) REVERT: M 370 ASN cc_start: 0.2092 (OUTLIER) cc_final: 0.1740 (p0) REVERT: M 395 MET cc_start: 0.1377 (ppp) cc_final: 0.0069 (ppp) REVERT: N 370 TRP cc_start: 0.2533 (t-100) cc_final: 0.2242 (t-100) REVERT: N 443 ILE cc_start: 0.1197 (OUTLIER) cc_final: 0.0258 (mt) outliers start: 66 outliers final: 42 residues processed: 272 average time/residue: 1.0836 time to fit residues: 366.5174 Evaluate side-chains 274 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 224 time to evaluate : 3.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 407 ARG Chi-restraints excluded: chain F residue 414 ASN Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 463 THR Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 370 ASN Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 435 MET Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain M residue 370 ASN Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 113 ARG Chi-restraints excluded: chain N residue 429 ILE Chi-restraints excluded: chain N residue 443 ILE Chi-restraints excluded: chain N residue 490 LEU Chi-restraints excluded: chain N residue 495 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 306 optimal weight: 2.9990 chunk 323 optimal weight: 0.6980 chunk 294 optimal weight: 1.9990 chunk 314 optimal weight: 4.9990 chunk 189 optimal weight: 0.2980 chunk 136 optimal weight: 30.0000 chunk 246 optimal weight: 0.0980 chunk 96 optimal weight: 0.0170 chunk 284 optimal weight: 2.9990 chunk 297 optimal weight: 0.7980 chunk 313 optimal weight: 7.9990 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN L 251 HIS ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 205 GLN ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3874 moved from start: 0.7301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32370 Z= 0.174 Angle : 0.594 17.179 44449 Z= 0.305 Chirality : 0.041 0.353 4901 Planarity : 0.004 0.051 5060 Dihedral : 18.210 179.902 5854 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.03 % Allowed : 16.73 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.78 (0.14), residues: 3386 helix: 1.22 (0.16), residues: 1131 sheet: -0.51 (0.21), residues: 608 loop : -1.83 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.002 TRP I 20 HIS 0.004 0.001 HIS L 207 PHE 0.030 0.001 PHE N 53 TYR 0.020 0.001 TYR M 210 ARG 0.012 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 228 time to evaluate : 3.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: 0.0228 (mmm) cc_final: -0.1322 (mmm) REVERT: A 378 LEU cc_start: 0.1228 (OUTLIER) cc_final: 0.0914 (tp) REVERT: E 6 PHE cc_start: 0.5492 (t80) cc_final: 0.4026 (t80) REVERT: F 1 MET cc_start: 0.2555 (mmm) cc_final: 0.2016 (mmm) REVERT: F 14 PHE cc_start: 0.5492 (m-80) cc_final: 0.4503 (m-80) REVERT: F 223 ILE cc_start: 0.6750 (OUTLIER) cc_final: 0.6487 (mm) REVERT: I 395 MET cc_start: 0.3954 (OUTLIER) cc_final: 0.3599 (pp-130) REVERT: L 370 TRP cc_start: 0.1278 (t-100) cc_final: 0.0742 (t-100) REVERT: N 24 ARG cc_start: 0.6163 (mpp80) cc_final: 0.5859 (mtm180) REVERT: N 113 ARG cc_start: 0.3553 (OUTLIER) cc_final: 0.2730 (mmm-85) REVERT: N 443 ILE cc_start: 0.1230 (OUTLIER) cc_final: 0.0274 (mt) outliers start: 62 outliers final: 38 residues processed: 269 average time/residue: 1.0675 time to fit residues: 358.4638 Evaluate side-chains 265 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 222 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 407 ARG Chi-restraints excluded: chain F residue 414 ASN Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 463 THR Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 258 THR Chi-restraints excluded: chain L residue 435 MET Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 113 ARG Chi-restraints excluded: chain N residue 429 ILE Chi-restraints excluded: chain N residue 443 ILE Chi-restraints excluded: chain N residue 490 LEU Chi-restraints excluded: chain N residue 495 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 206 optimal weight: 10.0000 chunk 332 optimal weight: 1.9990 chunk 202 optimal weight: 0.1980 chunk 157 optimal weight: 0.4980 chunk 231 optimal weight: 0.0030 chunk 348 optimal weight: 4.9990 chunk 320 optimal weight: 0.6980 chunk 277 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 214 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN L 18 GLN ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3890 moved from start: 0.7440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32370 Z= 0.185 Angle : 0.610 17.024 44449 Z= 0.313 Chirality : 0.042 0.335 4901 Planarity : 0.004 0.051 5060 Dihedral : 18.194 179.901 5854 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.80 % Allowed : 17.15 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.74 (0.15), residues: 3386 helix: 1.23 (0.16), residues: 1131 sheet: -0.54 (0.21), residues: 654 loop : -1.79 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.002 TRP A 20 HIS 0.004 0.001 HIS L 207 PHE 0.033 0.001 PHE E 120 TYR 0.021 0.001 TYR M 210 ARG 0.003 0.000 ARG I 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 223 time to evaluate : 2.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: 0.0176 (mmm) cc_final: -0.1360 (mmm) REVERT: A 378 LEU cc_start: 0.1241 (OUTLIER) cc_final: 0.0993 (tp) REVERT: E 6 PHE cc_start: 0.5519 (t80) cc_final: 0.3955 (t80) REVERT: F 1 MET cc_start: 0.2582 (mmm) cc_final: 0.2055 (mmm) REVERT: F 14 PHE cc_start: 0.5575 (m-80) cc_final: 0.4455 (m-80) REVERT: F 136 VAL cc_start: 0.2397 (OUTLIER) cc_final: 0.1991 (t) REVERT: F 223 ILE cc_start: 0.6762 (OUTLIER) cc_final: 0.6481 (mm) REVERT: I 370 ASN cc_start: 0.4777 (OUTLIER) cc_final: 0.4529 (t0) REVERT: I 395 MET cc_start: 0.4101 (OUTLIER) cc_final: 0.3752 (pp-130) REVERT: L 370 TRP cc_start: 0.1253 (t-100) cc_final: 0.0779 (t-100) REVERT: M 15 ASN cc_start: 0.1752 (OUTLIER) cc_final: 0.1295 (m-40) REVERT: N 19 LYS cc_start: 0.6998 (ttmm) cc_final: 0.6424 (mppt) REVERT: N 24 ARG cc_start: 0.6172 (mpp80) cc_final: 0.5873 (mtm180) REVERT: N 113 ARG cc_start: 0.3575 (OUTLIER) cc_final: 0.2662 (mmm-85) REVERT: N 370 TRP cc_start: 0.2576 (t-100) cc_final: 0.2017 (t-100) REVERT: N 443 ILE cc_start: 0.1260 (OUTLIER) cc_final: 0.0509 (mt) outliers start: 55 outliers final: 36 residues processed: 265 average time/residue: 1.0567 time to fit residues: 350.3852 Evaluate side-chains 262 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 218 time to evaluate : 3.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 407 ARG Chi-restraints excluded: chain F residue 414 ASN Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 463 THR Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 370 ASN Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain L residue 258 THR Chi-restraints excluded: chain L residue 435 MET Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain M residue 15 ASN Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 113 ARG Chi-restraints excluded: chain N residue 429 ILE Chi-restraints excluded: chain N residue 443 ILE Chi-restraints excluded: chain N residue 490 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 220 optimal weight: 1.9990 chunk 295 optimal weight: 30.0000 chunk 85 optimal weight: 0.1980 chunk 256 optimal weight: 5.9990 chunk 40 optimal weight: 0.1980 chunk 77 optimal weight: 0.9990 chunk 278 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 285 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 GLN ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5367 r_free = 0.5367 target = 0.284527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5099 r_free = 0.5099 target = 0.251798 restraints weight = 46376.762| |-----------------------------------------------------------------------------| r_work (start): 0.5078 rms_B_bonded: 2.64 r_work: 0.4909 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4729 moved from start: 0.7832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32370 Z= 0.255 Angle : 0.674 22.259 44449 Z= 0.346 Chirality : 0.044 0.292 4901 Planarity : 0.005 0.055 5060 Dihedral : 18.250 179.341 5854 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 1.73 % Allowed : 17.58 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.96 (0.14), residues: 3386 helix: 0.95 (0.16), residues: 1127 sheet: -0.41 (0.22), residues: 597 loop : -1.90 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.123 0.002 TRP A 20 HIS 0.006 0.001 HIS L 217 PHE 0.041 0.002 PHE E 120 TYR 0.023 0.001 TYR M 210 ARG 0.009 0.000 ARG E 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8939.41 seconds wall clock time: 159 minutes 7.33 seconds (9547.33 seconds total)