Starting phenix.real_space_refine on Fri Jun 27 06:11:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8spo_40680/06_2025/8spo_40680_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8spo_40680/06_2025/8spo_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/cci-nas-00/data/ceres_data/8spo_40680/06_2025/8spo_40680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8spo_40680/06_2025/8spo_40680.map" model { file = "/net/cci-nas-00/data/ceres_data/8spo_40680/06_2025/8spo_40680_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8spo_40680/06_2025/8spo_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. Time to flip 2 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 19.96, per 1000 atoms: 0.64 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 - 3.00 Amino acid : True - 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.88 Conformation dependent library (CDL) restraints added in 3.5 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: 11.04 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: 11.83 Time building geometry restraints manager: 9.29 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: 0.00 - 1.81: 43528 1.81 - 3.61: 811 3.61 - 5.42: 94 5.42 - 7.22: 11 7.22 - 9.03: 5 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: 32 1.25 - 2.16: 190 2.16 - 3.07: 20655 3.07 - 3.99: 79333 3.99 - 4.90: 151707 Warning: very small nonbonded interaction distances. Nonbonded interactions: 251917 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=" 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 nonbonded pdb=" CG ASP L 137 " pdb=" OD1 ASN N 135 " model vdw 0.666 3.270 ... (remaining 251912 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 7.880 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: 0.020 Extract box with map and model: 1.320 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 77.210 Find NCS groups from input model: 1.520 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:13.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.530 ------------------------------------------------------------------------------- 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 : 0.006 0.671 32375 Z= 0.575 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 Details of bonding type rmsd hydrogen bonds : bond 0.18460 ( 1195) hydrogen bonds : angle 7.16918 ( 3388) covalent geometry : bond 0.00363 (32370) covalent geometry : angle 0.59720 (44449) Misc. bond : bond 0.43189 ( 5) *********************** 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 to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 3.133 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: 1.2533 time to fit residues: 468.2327 Evaluate side-chains 249 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 3.147 ------------------------------------------------------------------------------- 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: 20.0000 chunk 265 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 274 optimal weight: 0.0970 chunk 106 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 204 optimal weight: 6.9990 chunk 317 optimal weight: 20.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN F 16 HIS F 18 GLN F 327 GLN L 349 GLN ** L 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 ASN N 135 ASN ** N 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 217 HIS N 329 HIS ** N 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 446 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5460 r_free = 0.5460 target = 0.295489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5178 r_free = 0.5178 target = 0.261165 restraints weight = 48091.022| |-----------------------------------------------------------------------------| r_work (start): 0.5151 rms_B_bonded: 2.92 r_work: 0.5015 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.5015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4389 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 32375 Z= 0.250 Angle : 0.816 18.909 44449 Z= 0.425 Chirality : 0.050 0.299 4901 Planarity : 0.006 0.065 5060 Dihedral : 18.808 179.028 5854 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.76 % Allowed : 6.93 % Favored : 91.31 % 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: -1.19 (0.14), residues: 3386 helix: 0.77 (0.16), residues: 1115 sheet: -0.70 (0.20), residues: 661 loop : -1.99 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP N 139 HIS 0.011 0.002 HIS B 360 PHE 0.030 0.003 PHE L 53 TYR 0.037 0.002 TYR N 505 ARG 0.013 0.001 ARG L 481 Details of bonding type rmsd hydrogen bonds : bond 0.05593 ( 1195) hydrogen bonds : angle 5.55947 ( 3388) covalent geometry : bond 0.00544 (32370) covalent geometry : angle 0.81637 (44449) Misc. bond : bond 0.00654 ( 5) *********************** 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 330 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 276 time to evaluate : 4.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.2321 (OUTLIER) cc_final: 0.1877 (mtmm) REVERT: A 277 MET cc_start: -0.1728 (mmm) cc_final: -0.2392 (mmm) REVERT: A 395 MET cc_start: 0.2001 (OUTLIER) cc_final: -0.0046 (tpp) REVERT: B 6 TYR cc_start: 0.4952 (t80) cc_final: 0.4672 (t80) REVERT: B 87 GLU cc_start: 0.5708 (pm20) cc_final: 0.5281 (pm20) REVERT: B 345 SER cc_start: 0.5720 (t) cc_final: 0.5234 (m) REVERT: E 35 ASP cc_start: 0.4922 (OUTLIER) cc_final: 0.4543 (p0) REVERT: E 274 GLU cc_start: 0.4320 (OUTLIER) cc_final: 0.3987 (mp0) REVERT: F 1 MET cc_start: 0.3444 (mmm) cc_final: 0.3105 (mmm) REVERT: F 14 PHE cc_start: 0.5638 (m-80) cc_final: 0.4984 (m-80) REVERT: F 223 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7191 (mm) REVERT: F 254 TRP cc_start: 0.4395 (m100) cc_final: 0.4129 (m100) REVERT: I 336 MET cc_start: 0.4977 (mpt) cc_final: 0.4538 (mpt) REVERT: L 384 VAL cc_start: 0.5553 (OUTLIER) cc_final: 0.5257 (t) REVERT: M 122 MET cc_start: 0.6270 (mmp) cc_final: 0.6030 (mmm) REVERT: N 19 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6680 (mptp) REVERT: N 205 GLN cc_start: 0.6359 (mm-40) cc_final: 0.5769 (mp10) REVERT: N 206 PHE cc_start: 0.5843 (t80) cc_final: 0.5507 (t80) outliers start: 54 outliers final: 17 residues processed: 308 average time/residue: 1.5993 time to fit residues: 613.2269 Evaluate side-chains 267 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 243 time to evaluate : 3.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 341 GLN 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 35 ASP Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain F residue 29 LEU 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 L residue 384 VAL Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 19 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 36 optimal weight: 2.9990 chunk 337 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 285 optimal weight: 4.9990 chunk 301 optimal weight: 1.9990 chunk 349 optimal weight: 3.9990 chunk 191 optimal weight: 7.9990 chunk 310 optimal weight: 1.9990 chunk 297 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN A 314 GLN A 358 HIS ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN B 207 HIS B 217 HIS B 327 GLN ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS B 430 GLN F 34 ASN F 66 ASN F 205 GLN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 358 HIS N 66 ASN N 129 ASN ** N 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 360 HIS N 430 GLN N 439 ASN N 454 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5375 r_free = 0.5375 target = 0.284450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5109 r_free = 0.5109 target = 0.251619 restraints weight = 46731.260| |-----------------------------------------------------------------------------| r_work (start): 0.5070 rms_B_bonded: 2.45 r_work: 0.4899 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4710 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 32375 Z= 0.299 Angle : 0.841 27.749 44449 Z= 0.444 Chirality : 0.051 0.259 4901 Planarity : 0.006 0.082 5060 Dihedral : 18.919 178.252 5854 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.61 % Allowed : 10.65 % Favored : 86.74 % 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: -1.65 (0.14), residues: 3386 helix: 0.25 (0.15), residues: 1125 sheet: -0.87 (0.21), residues: 606 loop : -2.18 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP E 20 HIS 0.010 0.002 HIS L 217 PHE 0.040 0.003 PHE I 120 TYR 0.030 0.003 TYR N 65 ARG 0.012 0.001 ARG L 481 Details of bonding type rmsd hydrogen bonds : bond 0.06463 ( 1195) hydrogen bonds : angle 5.91041 ( 3388) covalent geometry : bond 0.00667 (32370) covalent geometry : angle 0.84094 (44449) Misc. bond : bond 0.00689 ( 5) *********************** 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 351 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 271 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ARG cc_start: -0.0807 (OUTLIER) cc_final: -0.1493 (mmp80) REVERT: A 277 MET cc_start: -0.1365 (mmm) cc_final: -0.2167 (mmm) REVERT: A 328 LYS cc_start: 0.6681 (mmtm) cc_final: 0.6470 (tttt) REVERT: A 395 MET cc_start: 0.2607 (OUTLIER) cc_final: -0.0376 (tmt) REVERT: B 356 GLU cc_start: 0.5795 (tm-30) cc_final: 0.5565 (tm-30) REVERT: E 36 ILE cc_start: 0.6069 (OUTLIER) cc_final: 0.5817 (pt) REVERT: E 395 MET cc_start: -0.1017 (OUTLIER) cc_final: -0.1359 (ptm) REVERT: F 1 MET cc_start: 0.3574 (mmm) cc_final: 0.3113 (mmm) REVERT: F 14 PHE cc_start: 0.6075 (m-80) cc_final: 0.4639 (m-80) REVERT: F 254 TRP cc_start: 0.4640 (m100) cc_final: 0.4400 (m100) REVERT: F 325 ASN cc_start: 0.7591 (t0) cc_final: 0.7359 (t0) REVERT: I 336 MET cc_start: 0.5309 (mpt) cc_final: 0.4787 (mpt) REVERT: L 139 TRP cc_start: 0.5926 (m100) cc_final: 0.5666 (m100) REVERT: L 419 PHE cc_start: 0.4402 (m-80) cc_final: 0.4161 (m-80) REVERT: M 122 MET cc_start: 0.6623 (mmp) cc_final: 0.6273 (mmm) REVERT: N 19 LYS cc_start: 0.7394 (mtpm) cc_final: 0.6605 (mmtp) REVERT: N 332 PRO cc_start: 0.4701 (Cg_endo) cc_final: 0.4478 (Cg_exo) REVERT: N 370 TRP cc_start: 0.3366 (t-100) cc_final: 0.2890 (t-100) outliers start: 80 outliers final: 36 residues processed: 325 average time/residue: 1.1146 time to fit residues: 446.1438 Evaluate side-chains 285 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 412 VAL 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 36 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 395 MET Chi-restraints excluded: chain F residue 29 LEU 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 465 LEU 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 65 SER Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain L residue 447 LYS Chi-restraints excluded: chain L residue 479 THR 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 M residue 57 THR Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 256 ILE Chi-restraints excluded: chain N residue 357 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 65 optimal weight: 0.7980 chunk 218 optimal weight: 0.7980 chunk 305 optimal weight: 0.3980 chunk 219 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN I 254 ASN L 251 HIS L 349 GLN ** L 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 341 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5393 r_free = 0.5393 target = 0.287121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5108 r_free = 0.5108 target = 0.252120 restraints weight = 47321.229| |-----------------------------------------------------------------------------| r_work (start): 0.5072 rms_B_bonded: 3.00 r_work: 0.4908 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4675 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32375 Z= 0.163 Angle : 0.655 23.726 44449 Z= 0.344 Chirality : 0.043 0.194 4901 Planarity : 0.005 0.062 5060 Dihedral : 18.621 178.209 5854 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.35 % Allowed : 13.26 % Favored : 84.38 % 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: -1.22 (0.14), residues: 3386 helix: 0.83 (0.15), residues: 1122 sheet: -0.73 (0.21), residues: 609 loop : -2.07 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 20 HIS 0.005 0.001 HIS L 207 PHE 0.027 0.002 PHE I 45 TYR 0.015 0.001 TYR N 65 ARG 0.006 0.000 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.04549 ( 1195) hydrogen bonds : angle 5.27954 ( 3388) covalent geometry : bond 0.00358 (32370) covalent geometry : angle 0.65509 (44449) Misc. bond : bond 0.00546 ( 5) *********************** 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 323 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 251 time to evaluate : 2.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: -0.1005 (mmm) cc_final: -0.2094 (mmm) REVERT: A 392 TYR cc_start: 0.6255 (OUTLIER) cc_final: 0.5650 (p90) REVERT: A 395 MET cc_start: 0.2484 (OUTLIER) cc_final: -0.0181 (tmt) REVERT: B 1 MET cc_start: 0.2556 (mmp) cc_final: 0.2122 (mmp) REVERT: B 327 GLN cc_start: 0.4931 (OUTLIER) cc_final: 0.3814 (mp10) REVERT: B 356 GLU cc_start: 0.5882 (tm-30) cc_final: 0.5574 (tm-30) REVERT: B 370 TRP cc_start: 0.3326 (t-100) cc_final: 0.2910 (t-100) REVERT: F 1 MET cc_start: 0.3584 (mmm) cc_final: 0.3154 (mmm) REVERT: F 14 PHE cc_start: 0.5816 (m-80) cc_final: 0.4350 (m-80) REVERT: I 135 PHE cc_start: 0.6231 (m-10) cc_final: 0.5802 (m-10) REVERT: I 336 MET cc_start: 0.5342 (mpt) cc_final: 0.4748 (mpt) REVERT: L 14 PHE cc_start: 0.6234 (m-80) cc_final: 0.5789 (m-80) REVERT: L 419 PHE cc_start: 0.4372 (m-80) cc_final: 0.3995 (m-80) REVERT: M 15 ASN cc_start: 0.1753 (OUTLIER) cc_final: 0.1366 (m-40) REVERT: M 168 GLU cc_start: 0.5277 (tp30) cc_final: 0.4750 (tp30) REVERT: N 19 LYS cc_start: 0.7370 (mtpm) cc_final: 0.6705 (mptt) REVERT: N 365 PHE cc_start: 0.0600 (OUTLIER) cc_final: -0.2506 (m-80) outliers start: 72 outliers final: 33 residues processed: 302 average time/residue: 1.0534 time to fit residues: 397.3673 Evaluate side-chains 274 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 327 GLN 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 E residue 123 SER 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 298 CYS 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 491 THR Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 121 LYS Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 349 GLN Chi-restraints excluded: chain L residue 447 LYS Chi-restraints excluded: chain L residue 460 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain M residue 5 ILE 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 370 ASN Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 365 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 53 optimal weight: 0.3980 chunk 157 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 300 optimal weight: 9.9990 chunk 66 optimal weight: 0.4980 chunk 176 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 297 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN F 325 ASN ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 349 GLN ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN ** N 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5367 r_free = 0.5367 target = 0.283842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5099 r_free = 0.5099 target = 0.250763 restraints weight = 46486.367| |-----------------------------------------------------------------------------| r_work (start): 0.5062 rms_B_bonded: 2.56 r_work: 0.4897 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4731 moved from start: 0.6535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 32375 Z= 0.212 Angle : 0.724 26.778 44449 Z= 0.377 Chirality : 0.046 0.218 4901 Planarity : 0.005 0.064 5060 Dihedral : 18.560 177.603 5854 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.91 % Allowed : 14.67 % Favored : 82.42 % 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: -1.39 (0.14), residues: 3386 helix: 0.61 (0.15), residues: 1129 sheet: -0.80 (0.21), residues: 626 loop : -2.13 (0.14), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP A 20 HIS 0.008 0.001 HIS L 217 PHE 0.029 0.002 PHE E 120 TYR 0.024 0.002 TYR B 6 ARG 0.008 0.001 ARG A 276 Details of bonding type rmsd hydrogen bonds : bond 0.05132 ( 1195) hydrogen bonds : angle 5.49657 ( 3388) covalent geometry : bond 0.00471 (32370) covalent geometry : angle 0.72447 (44449) Misc. bond : bond 0.00604 ( 5) *********************** 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 352 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 263 time to evaluate : 3.071 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: -0.1175 (mmm) cc_final: -0.2063 (mmm) REVERT: A 395 MET cc_start: 0.2225 (OUTLIER) cc_final: -0.0244 (tmt) REVERT: B 6 TYR cc_start: 0.5004 (t80) cc_final: 0.4677 (t80) REVERT: B 356 GLU cc_start: 0.5881 (tm-30) cc_final: 0.5562 (tm-30) REVERT: B 370 TRP cc_start: 0.3868 (t-100) cc_final: 0.3243 (t-100) REVERT: F 1 MET cc_start: 0.3407 (mmm) cc_final: 0.2901 (mmm) REVERT: F 14 PHE cc_start: 0.5980 (m-80) cc_final: 0.4832 (m-80) REVERT: F 283 LEU cc_start: 0.4766 (OUTLIER) cc_final: 0.4400 (tp) REVERT: I 37 LEU cc_start: 0.7155 (mm) cc_final: 0.6870 (mm) REVERT: I 122 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6857 (ptp) REVERT: I 135 PHE cc_start: 0.6191 (m-10) cc_final: 0.5786 (m-10) REVERT: I 323 ILE cc_start: 0.7179 (pt) cc_final: 0.6856 (mt) REVERT: I 336 MET cc_start: 0.5493 (mpt) cc_final: 0.5039 (mpt) REVERT: I 370 ASN cc_start: 0.4705 (OUTLIER) cc_final: 0.4309 (t0) REVERT: L 139 TRP cc_start: 0.5938 (m100) cc_final: 0.5297 (t-100) REVERT: L 320 TRP cc_start: 0.5329 (m100) cc_final: 0.5000 (m-10) REVERT: L 384 VAL cc_start: 0.5836 (OUTLIER) cc_final: 0.5616 (t) REVERT: M 15 ASN cc_start: 0.1809 (OUTLIER) cc_final: 0.1273 (t0) REVERT: M 370 ASN cc_start: 0.1666 (OUTLIER) cc_final: 0.1449 (t0) REVERT: N 19 LYS cc_start: 0.7345 (mtpm) cc_final: 0.6648 (mptt) REVERT: N 365 PHE cc_start: 0.0497 (OUTLIER) cc_final: -0.2789 (m-80) REVERT: N 370 TRP cc_start: 0.3313 (m100) cc_final: 0.2484 (m100) outliers start: 89 outliers final: 47 residues processed: 330 average time/residue: 1.1097 time to fit residues: 453.9232 Evaluate side-chains 306 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 251 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 412 VAL 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 112 ILE Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 405 ASN Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 283 LEU 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 445 ILE Chi-restraints excluded: chain F residue 459 ILE 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 40 ASP Chi-restraints excluded: chain I residue 46 TRP Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain I residue 121 LYS Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 370 ASN Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 384 VAL Chi-restraints excluded: chain L residue 435 MET Chi-restraints excluded: chain L residue 447 LYS Chi-restraints excluded: chain L residue 460 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain M residue 5 ILE 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 309 MET Chi-restraints excluded: chain M residue 370 ASN Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 256 ILE Chi-restraints excluded: chain N residue 365 PHE Chi-restraints excluded: chain N residue 377 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 126 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 315 optimal weight: 0.9980 chunk 161 optimal weight: 0.3980 chunk 245 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** B 409 ASN F 325 ASN F 327 GLN I 69 ASN I 254 ASN ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 446 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5382 r_free = 0.5382 target = 0.286488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5094 r_free = 0.5094 target = 0.251413 restraints weight = 46714.292| |-----------------------------------------------------------------------------| r_work (start): 0.5069 rms_B_bonded: 2.73 r_work: 0.4921 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4671 moved from start: 0.6742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 32375 Z= 0.149 Angle : 0.643 22.732 44449 Z= 0.332 Chirality : 0.043 0.196 4901 Planarity : 0.004 0.056 5060 Dihedral : 18.419 178.355 5854 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.35 % Allowed : 16.11 % Favored : 81.54 % 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: -1.13 (0.14), residues: 3386 helix: 0.91 (0.16), residues: 1135 sheet: -0.70 (0.21), residues: 624 loop : -2.04 (0.14), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP A 20 HIS 0.005 0.001 HIS L 207 PHE 0.028 0.002 PHE L 30 TYR 0.021 0.001 TYR B 6 ARG 0.007 0.000 ARG E 19 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 1195) hydrogen bonds : angle 5.09910 ( 3388) covalent geometry : bond 0.00328 (32370) covalent geometry : angle 0.64287 (44449) Misc. bond : bond 0.00537 ( 5) *********************** 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 325 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 253 time to evaluate : 3.268 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: -0.1155 (mmm) cc_final: -0.1910 (mmm) REVERT: A 395 MET cc_start: 0.2176 (OUTLIER) cc_final: -0.0301 (tmt) REVERT: B 1 MET cc_start: 0.2837 (mmp) cc_final: 0.2484 (mmp) REVERT: B 6 TYR cc_start: 0.4971 (t80) cc_final: 0.4738 (t80) REVERT: B 356 GLU cc_start: 0.5876 (tm-30) cc_final: 0.5529 (tm-30) REVERT: B 370 TRP cc_start: 0.3717 (t-100) cc_final: 0.2617 (t-100) REVERT: F 1 MET cc_start: 0.3474 (mmm) cc_final: 0.2959 (mmm) REVERT: F 14 PHE cc_start: 0.5629 (m-80) cc_final: 0.5108 (m-80) REVERT: F 283 LEU cc_start: 0.4882 (OUTLIER) cc_final: 0.4530 (tp) REVERT: I 323 ILE cc_start: 0.7103 (pt) cc_final: 0.6819 (mt) REVERT: I 336 MET cc_start: 0.5439 (mpt) cc_final: 0.4972 (mpt) REVERT: I 370 ASN cc_start: 0.4604 (OUTLIER) cc_final: 0.4340 (t0) REVERT: L 139 TRP cc_start: 0.6064 (m100) cc_final: 0.5626 (t-100) REVERT: L 460 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.5658 (tt) REVERT: M 15 ASN cc_start: 0.1792 (OUTLIER) cc_final: 0.1409 (m-40) REVERT: M 370 ASN cc_start: 0.1490 (OUTLIER) cc_final: 0.1258 (p0) REVERT: N 19 LYS cc_start: 0.7336 (mtpm) cc_final: 0.6678 (mptt) REVERT: N 205 GLN cc_start: 0.6699 (mm-40) cc_final: 0.6160 (mm110) REVERT: N 216 LYS cc_start: 0.5523 (OUTLIER) cc_final: 0.5312 (pttp) REVERT: N 365 PHE cc_start: 0.0510 (OUTLIER) cc_final: -0.2661 (m-80) REVERT: N 370 TRP cc_start: 0.3047 (m100) cc_final: 0.1968 (m100) outliers start: 72 outliers final: 33 residues processed: 307 average time/residue: 1.1009 time to fit residues: 422.5087 Evaluate side-chains 282 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 241 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 407 ARG Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain F residue 465 LEU 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 63 VAL Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 327 SER Chi-restraints excluded: chain I residue 370 ASN Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 219 ILE Chi-restraints excluded: chain L residue 447 LYS Chi-restraints excluded: chain L residue 460 LEU 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 309 MET Chi-restraints excluded: chain M residue 370 ASN Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 216 LYS Chi-restraints excluded: chain N residue 365 PHE Chi-restraints excluded: chain N residue 367 HIS Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain N residue 429 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 329 optimal weight: 0.1980 chunk 163 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 234 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 184 optimal weight: 0.6980 chunk 296 optimal weight: 5.9990 chunk 119 optimal weight: 50.0000 chunk 239 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 ASN F 325 ASN ** M 15 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 = 0.5380 r_free = 0.5380 target = 0.285539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5114 r_free = 0.5114 target = 0.252539 restraints weight = 46870.275| |-----------------------------------------------------------------------------| r_work (start): 0.5082 rms_B_bonded: 2.59 r_work: 0.4929 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4668 moved from start: 0.7053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32375 Z= 0.157 Angle : 0.656 22.872 44449 Z= 0.337 Chirality : 0.043 0.211 4901 Planarity : 0.005 0.056 5060 Dihedral : 18.377 178.506 5854 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.26 % Favored : 93.71 % Rotamer: Outliers : 2.45 % Allowed : 16.82 % Favored : 80.73 % 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: -1.08 (0.14), residues: 3386 helix: 0.98 (0.16), residues: 1133 sheet: -0.60 (0.21), residues: 613 loop : -2.05 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.099 0.002 TRP A 20 HIS 0.005 0.001 HIS E 340 PHE 0.027 0.002 PHE I 45 TYR 0.020 0.001 TYR B 6 ARG 0.006 0.000 ARG E 19 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 1195) hydrogen bonds : angle 5.08606 ( 3388) covalent geometry : bond 0.00346 (32370) covalent geometry : angle 0.65593 (44449) Misc. bond : bond 0.00506 ( 5) *********************** 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 322 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 247 time to evaluate : 2.987 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 202 GLU cc_start: 0.5615 (OUTLIER) cc_final: 0.5304 (pm20) REVERT: A 277 MET cc_start: -0.1085 (mmm) cc_final: -0.1877 (mmm) REVERT: A 395 MET cc_start: 0.2075 (OUTLIER) cc_final: -0.0530 (tmt) REVERT: B 1 MET cc_start: 0.2701 (mmp) cc_final: 0.2411 (mmp) REVERT: B 6 TYR cc_start: 0.4972 (t80) cc_final: 0.4765 (t80) REVERT: B 356 GLU cc_start: 0.5824 (tm-30) cc_final: 0.5471 (tm-30) REVERT: B 370 TRP cc_start: 0.3821 (t-100) cc_final: 0.2752 (t-100) REVERT: F 1 MET cc_start: 0.3436 (mmm) cc_final: 0.2824 (mmm) REVERT: F 14 PHE cc_start: 0.5812 (m-80) cc_final: 0.5225 (m-80) REVERT: F 283 LEU cc_start: 0.4905 (OUTLIER) cc_final: 0.4553 (tp) REVERT: F 364 ARG cc_start: 0.5410 (OUTLIER) cc_final: 0.4332 (ppt170) REVERT: F 497 LYS cc_start: 0.6655 (ttpp) cc_final: 0.6420 (ttmm) REVERT: I 85 LYS cc_start: 0.5988 (ptmt) cc_final: 0.4568 (pttt) REVERT: I 323 ILE cc_start: 0.7197 (pt) cc_final: 0.6873 (mt) REVERT: I 336 MET cc_start: 0.5470 (mpt) cc_final: 0.4984 (mpt) REVERT: I 370 ASN cc_start: 0.4614 (OUTLIER) cc_final: 0.4344 (t0) REVERT: L 139 TRP cc_start: 0.5981 (m100) cc_final: 0.5497 (t-100) REVERT: M 15 ASN cc_start: 0.1565 (OUTLIER) cc_final: 0.1146 (m-40) REVERT: M 370 ASN cc_start: 0.1407 (OUTLIER) cc_final: 0.1173 (t0) REVERT: N 19 LYS cc_start: 0.7278 (mtpm) cc_final: 0.6651 (mptt) REVERT: N 205 GLN cc_start: 0.6704 (mm-40) cc_final: 0.6453 (mm-40) REVERT: N 216 LYS cc_start: 0.5544 (OUTLIER) cc_final: 0.5303 (pttp) REVERT: N 256 ILE cc_start: 0.5196 (OUTLIER) cc_final: 0.4986 (tt) REVERT: N 365 PHE cc_start: 0.0389 (OUTLIER) cc_final: -0.2867 (m-80) REVERT: N 370 TRP cc_start: 0.3186 (m100) cc_final: 0.2682 (m100) outliers start: 75 outliers final: 45 residues processed: 305 average time/residue: 1.3617 time to fit residues: 520.9146 Evaluate side-chains 298 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 243 time to evaluate : 3.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 395 MET 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 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 E residue 112 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 F residue 44 ILE Chi-restraints excluded: chain F residue 274 VAL 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 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 65 SER Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 327 SER Chi-restraints excluded: chain I residue 370 ASN Chi-restraints excluded: chain L residue 7 ILE Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 219 ILE 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 470 CYS Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain M residue 5 ILE 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 309 MET Chi-restraints excluded: chain M residue 370 ASN Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 216 LYS Chi-restraints excluded: chain N residue 256 ILE Chi-restraints excluded: chain N residue 365 PHE Chi-restraints excluded: chain N residue 367 HIS Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain N residue 429 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 136 optimal weight: 30.0000 chunk 42 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 188 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 233 optimal weight: 1.9990 chunk 337 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 278 optimal weight: 0.9980 chunk 327 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 HIS ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 ASN M 3 ASN ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 329 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5372 r_free = 0.5372 target = 0.285171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5099 r_free = 0.5099 target = 0.250866 restraints weight = 46675.496| |-----------------------------------------------------------------------------| r_work (start): 0.5067 rms_B_bonded: 2.74 r_work: 0.4898 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4736 moved from start: 0.7414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32375 Z= 0.165 Angle : 0.666 23.088 44449 Z= 0.342 Chirality : 0.043 0.207 4901 Planarity : 0.005 0.056 5060 Dihedral : 18.322 178.880 5854 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.35 % Allowed : 17.45 % Favored : 80.20 % 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: -1.07 (0.14), residues: 3386 helix: 0.97 (0.16), residues: 1128 sheet: -0.48 (0.22), residues: 607 loop : -2.07 (0.14), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.108 0.002 TRP A 20 HIS 0.005 0.001 HIS L 207 PHE 0.033 0.002 PHE L 30 TYR 0.018 0.001 TYR B 6 ARG 0.010 0.000 ARG E 19 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 1195) hydrogen bonds : angle 5.12169 ( 3388) covalent geometry : bond 0.00367 (32370) covalent geometry : angle 0.66553 (44449) Misc. bond : bond 0.00585 ( 5) *********************** 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 320 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 248 time to evaluate : 3.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLU cc_start: 0.5589 (OUTLIER) cc_final: 0.5245 (pm20) REVERT: A 277 MET cc_start: -0.1044 (mmm) cc_final: -0.1873 (mmm) REVERT: A 395 MET cc_start: 0.2021 (OUTLIER) cc_final: -0.0684 (tmt) REVERT: B 370 TRP cc_start: 0.3771 (t-100) cc_final: 0.2716 (t-100) REVERT: E 6 PHE cc_start: 0.6070 (t80) cc_final: 0.4625 (t80) REVERT: F 1 MET cc_start: 0.3433 (mmm) cc_final: 0.2946 (mmm) REVERT: F 14 PHE cc_start: 0.5856 (m-80) cc_final: 0.5008 (m-80) REVERT: F 435 MET cc_start: -0.0193 (mpp) cc_final: -0.0398 (mpp) REVERT: I 323 ILE cc_start: 0.7191 (pt) cc_final: 0.6820 (mt) REVERT: I 336 MET cc_start: 0.5482 (mpt) cc_final: 0.5119 (mpt) REVERT: I 370 ASN cc_start: 0.4556 (OUTLIER) cc_final: 0.4281 (t0) REVERT: M 15 ASN cc_start: 0.1633 (OUTLIER) cc_final: 0.1224 (m-40) REVERT: M 370 ASN cc_start: 0.1565 (OUTLIER) cc_final: 0.1353 (t0) REVERT: N 19 LYS cc_start: 0.7372 (mtpm) cc_final: 0.6689 (mptt) REVERT: N 216 LYS cc_start: 0.5605 (OUTLIER) cc_final: 0.5360 (pttp) REVERT: N 256 ILE cc_start: 0.5271 (OUTLIER) cc_final: 0.5044 (tt) REVERT: N 365 PHE cc_start: 0.0314 (OUTLIER) cc_final: -0.1865 (m-80) REVERT: N 370 TRP cc_start: 0.3157 (m100) cc_final: 0.1733 (m100) outliers start: 72 outliers final: 49 residues processed: 303 average time/residue: 1.1913 time to fit residues: 453.7541 Evaluate side-chains 295 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 238 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 395 MET 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 412 VAL Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 112 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 F residue 44 ILE Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 407 ARG Chi-restraints excluded: chain F residue 459 ILE 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 F residue 504 LYS Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 327 SER Chi-restraints excluded: chain I residue 370 ASN Chi-restraints excluded: chain L residue 7 ILE Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 219 ILE Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain L residue 309 ASP Chi-restraints excluded: chain L residue 435 MET Chi-restraints excluded: chain L residue 447 LYS Chi-restraints excluded: chain L residue 470 CYS 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 121 LYS Chi-restraints excluded: chain M residue 309 MET 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 69 SER Chi-restraints excluded: chain N residue 216 LYS Chi-restraints excluded: chain N residue 256 ILE Chi-restraints excluded: chain N residue 365 PHE Chi-restraints excluded: chain N residue 367 HIS Chi-restraints excluded: chain N residue 369 GLU Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain N residue 381 THR Chi-restraints excluded: chain N residue 429 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 145 optimal weight: 5.9990 chunk 248 optimal weight: 0.1980 chunk 65 optimal weight: 0.0370 chunk 33 optimal weight: 0.7980 chunk 234 optimal weight: 0.7980 chunk 25 optimal weight: 0.0980 chunk 172 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 239 optimal weight: 0.4980 chunk 213 optimal weight: 5.9990 chunk 319 optimal weight: 0.9990 overall best weight: 0.3058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 ASN F 325 ASN ** F 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 349 GLN ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 341 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5402 r_free = 0.5402 target = 0.288794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5144 r_free = 0.5144 target = 0.255712 restraints weight = 47038.767| |-----------------------------------------------------------------------------| r_work (start): 0.5115 rms_B_bonded: 2.60 r_work: 0.4956 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4594 moved from start: 0.7457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32375 Z= 0.122 Angle : 0.621 17.495 44449 Z= 0.317 Chirality : 0.042 0.200 4901 Planarity : 0.004 0.054 5060 Dihedral : 18.249 179.922 5854 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.37 % Allowed : 19.08 % Favored : 79.55 % 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 (0.15), residues: 3386 helix: 1.20 (0.16), residues: 1137 sheet: -0.56 (0.21), residues: 646 loop : -1.93 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.002 TRP A 20 HIS 0.004 0.001 HIS L 207 PHE 0.032 0.001 PHE F 261 TYR 0.030 0.001 TYR B 6 ARG 0.004 0.000 ARG I 114 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 1195) hydrogen bonds : angle 4.78042 ( 3388) covalent geometry : bond 0.00266 (32370) covalent geometry : angle 0.62144 (44449) Misc. bond : bond 0.00473 ( 5) *********************** 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 288 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 246 time to evaluate : 2.968 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: -0.1016 (mmm) cc_final: -0.1820 (mmm) REVERT: A 395 MET cc_start: 0.1829 (OUTLIER) cc_final: -0.0818 (tmt) REVERT: B 25 ASP cc_start: 0.5217 (m-30) cc_final: 0.4873 (m-30) REVERT: B 356 GLU cc_start: 0.5786 (tm-30) cc_final: 0.5496 (tm-30) REVERT: B 486 ILE cc_start: 0.4663 (OUTLIER) cc_final: 0.4367 (tt) REVERT: E 6 PHE cc_start: 0.5935 (t80) cc_final: 0.4295 (t80) REVERT: F 1 MET cc_start: 0.3514 (mmm) cc_final: 0.2977 (mmm) REVERT: F 14 PHE cc_start: 0.5524 (m-80) cc_final: 0.5093 (m-80) REVERT: F 435 MET cc_start: -0.0163 (mpp) cc_final: -0.0393 (mpp) REVERT: I 323 ILE cc_start: 0.7058 (pt) cc_final: 0.6769 (mt) REVERT: I 336 MET cc_start: 0.5378 (mpt) cc_final: 0.4965 (mpt) REVERT: I 370 ASN cc_start: 0.4459 (OUTLIER) cc_final: 0.4182 (t0) REVERT: L 139 TRP cc_start: 0.5977 (m100) cc_final: 0.5524 (t-100) REVERT: M 5 ILE cc_start: 0.7615 (mt) cc_final: 0.7360 (pt) REVERT: N 19 LYS cc_start: 0.7249 (mtpm) cc_final: 0.6626 (mptt) REVERT: N 365 PHE cc_start: 0.0136 (OUTLIER) cc_final: -0.3290 (m-80) outliers start: 42 outliers final: 22 residues processed: 275 average time/residue: 1.1360 time to fit residues: 386.5098 Evaluate side-chains 264 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 238 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain E residue 16 ASP 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 F residue 407 ARG Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 370 ASN Chi-restraints excluded: chain L residue 219 ILE 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 121 LYS Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 365 PHE Chi-restraints excluded: chain N residue 367 HIS Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain N residue 429 ILE Chi-restraints excluded: chain N residue 435 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 34 optimal weight: 0.8980 chunk 262 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 333 optimal weight: 2.9990 chunk 304 optimal weight: 0.7980 chunk 178 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 140 optimal weight: 0.2980 chunk 246 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 340 HIS F 446 ASN L 349 GLN ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5375 r_free = 0.5375 target = 0.285327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5099 r_free = 0.5099 target = 0.250948 restraints weight = 46607.717| |-----------------------------------------------------------------------------| r_work (start): 0.5070 rms_B_bonded: 2.58 r_work: 0.4908 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4717 moved from start: 0.7740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 32375 Z= 0.167 Angle : 0.682 21.519 44449 Z= 0.349 Chirality : 0.043 0.212 4901 Planarity : 0.005 0.057 5060 Dihedral : 18.280 179.589 5854 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.40 % Allowed : 19.54 % Favored : 79.06 % 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: -0.94 (0.14), residues: 3386 helix: 1.06 (0.16), residues: 1131 sheet: -0.31 (0.22), residues: 592 loop : -2.02 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.111 0.003 TRP A 20 HIS 0.007 0.001 HIS L 217 PHE 0.040 0.002 PHE I 120 TYR 0.020 0.001 TYR A 225 ARG 0.008 0.000 ARG E 19 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 1195) hydrogen bonds : angle 5.04487 ( 3388) covalent geometry : bond 0.00375 (32370) covalent geometry : angle 0.68195 (44449) Misc. bond : bond 0.00546 ( 5) ********************** 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 285 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 242 time to evaluate : 3.650 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: -0.1101 (mmm) cc_final: -0.1900 (mmm) REVERT: A 395 MET cc_start: 0.1786 (OUTLIER) cc_final: -0.0933 (tmt) REVERT: B 25 ASP cc_start: 0.5334 (m-30) cc_final: 0.5011 (m-30) REVERT: B 132 GLU cc_start: 0.5379 (mt-10) cc_final: 0.5121 (mt-10) REVERT: B 249 GLU cc_start: 0.5205 (tp30) cc_final: 0.4720 (tp30) REVERT: F 1 MET cc_start: 0.3588 (mmm) cc_final: 0.3136 (mmm) REVERT: F 14 PHE cc_start: 0.5815 (m-80) cc_final: 0.5368 (m-80) REVERT: F 364 ARG cc_start: 0.5466 (OUTLIER) cc_final: 0.4341 (ppt170) REVERT: F 435 MET cc_start: -0.0026 (mpp) cc_final: -0.0278 (mpp) REVERT: I 85 LYS cc_start: 0.6057 (ptmt) cc_final: 0.4548 (pttt) REVERT: I 323 ILE cc_start: 0.7167 (pt) cc_final: 0.6834 (mt) REVERT: I 336 MET cc_start: 0.5428 (mpt) cc_final: 0.5043 (mpt) REVERT: I 370 ASN cc_start: 0.4420 (OUTLIER) cc_final: 0.4155 (t0) REVERT: L 328 TYR cc_start: 0.5932 (m-80) cc_final: 0.1658 (OUTLIER) REVERT: N 19 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6662 (mptt) REVERT: N 365 PHE cc_start: 0.0141 (OUTLIER) cc_final: -0.1902 (m-80) REVERT: N 370 TRP cc_start: 0.3196 (m100) cc_final: 0.1755 (m100) outliers start: 43 outliers final: 26 residues processed: 272 average time/residue: 1.1927 time to fit residues: 397.5443 Evaluate side-chains 270 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 407 ARG Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 370 ASN Chi-restraints excluded: chain L residue 7 ILE Chi-restraints excluded: chain L residue 219 ILE 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 121 LYS Chi-restraints excluded: chain M residue 309 MET Chi-restraints excluded: chain N residue 19 LYS Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 365 PHE Chi-restraints excluded: chain N residue 367 HIS Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain N residue 429 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 161 optimal weight: 0.0570 chunk 239 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 338 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 229 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 175 optimal weight: 2.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 349 GLN ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5381 r_free = 0.5381 target = 0.285964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5104 r_free = 0.5104 target = 0.251497 restraints weight = 46488.488| |-----------------------------------------------------------------------------| r_work (start): 0.5077 rms_B_bonded: 2.66 r_work: 0.4920 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4694 moved from start: 0.7852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32375 Z= 0.153 Angle : 0.678 20.603 44449 Z= 0.344 Chirality : 0.043 0.202 4901 Planarity : 0.004 0.056 5060 Dihedral : 18.293 179.690 5854 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.27 % Allowed : 19.83 % Favored : 78.90 % 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: 1.05 (0.16), residues: 1136 sheet: -0.54 (0.21), residues: 636 loop : -1.98 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.112 0.003 TRP I 20 HIS 0.010 0.001 HIS E 340 PHE 0.044 0.002 PHE A 17 TYR 0.014 0.001 TYR F 505 ARG 0.003 0.000 ARG I 54 Details of bonding type rmsd hydrogen bonds : bond 0.04129 ( 1195) hydrogen bonds : angle 4.99722 ( 3388) covalent geometry : bond 0.00341 (32370) covalent geometry : angle 0.67814 (44449) Misc. bond : bond 0.00593 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24858.25 seconds wall clock time: 433 minutes 16.05 seconds (25996.05 seconds total)