Starting phenix.real_space_refine on Mon Aug 25 23:12:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8spo_40680/08_2025/8spo_40680_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8spo_40680/08_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_40680/08_2025/8spo_40680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8spo_40680/08_2025/8spo_40680.map" model { file = "/net/cci-nas-00/data/ceres_data/8spo_40680/08_2025/8spo_40680_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8spo_40680/08_2025/8spo_40680_neut.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 7.83, per 1000 atoms: 0.25 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: 2.57 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 4.07 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: 7.57 Time building geometry restraints manager: 3.55 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: 7.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.690 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 32.880 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 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:7.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.850 ------------------------------------------------------------------------------- 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 : 11.02 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG F 407 TYR 0.044 0.001 TYR A 105 PHE 0.015 0.001 PHE F 14 TRP 0.019 0.001 TRP A 33 HIS 0.006 0.001 HIS M 188 Details of bonding type rmsd covalent geometry : bond 0.00363 (32370) covalent geometry : angle 0.59720 (44449) hydrogen bonds : bond 0.18460 ( 1195) hydrogen bonds : angle 7.16918 ( 3388) 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 : 1.041 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: -0.1429 (mmm) REVERT: B 307 ASN cc_start: 0.6718 (p0) cc_final: 0.6437 (p0) REVERT: B 345 SER cc_start: 0.4870 (t) cc_final: 0.4638 (m) REVERT: F 490 LEU cc_start: 0.6896 (pp) cc_final: 0.6694 (pp) REVERT: L 280 TYR cc_start: 0.1927 (m-80) cc_final: 0.1374 (m-80) outliers start: 0 outliers final: 1 residues processed: 308 average time/residue: 0.6186 time to fit residues: 231.0085 Evaluate side-chains 248 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 157 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.0770 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.0970 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.8338 ------------------------------------------------------------------------------- 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 B 446 ASN F 16 HIS F 18 GLN ** I 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 360 HIS N 135 ASN ** N 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 217 HIS ** N 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 446 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5497 r_free = 0.5497 target = 0.300627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5229 r_free = 0.5229 target = 0.267429 restraints weight = 49134.825| |-----------------------------------------------------------------------------| r_work (start): 0.5203 rms_B_bonded: 3.08 r_work: 0.5077 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.5077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4220 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 32375 Z= 0.202 Angle : 0.713 14.061 44449 Z= 0.373 Chirality : 0.046 0.256 4901 Planarity : 0.005 0.060 5060 Dihedral : 18.692 178.664 5856 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.34 % Allowed : 6.53 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.14), residues: 3386 helix: 1.05 (0.16), residues: 1145 sheet: -0.62 (0.20), residues: 661 loop : -1.97 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 481 TYR 0.027 0.002 TYR N 505 PHE 0.025 0.002 PHE E 45 TRP 0.023 0.002 TRP F 269 HIS 0.009 0.001 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00426 (32370) covalent geometry : angle 0.71277 (44449) hydrogen bonds : bond 0.05103 ( 1195) hydrogen bonds : angle 5.32875 ( 3388) Misc. bond : bond 0.00643 ( 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 308 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 267 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: -0.1670 (mmm) cc_final: -0.2202 (mmm) REVERT: A 395 MET cc_start: 0.2224 (OUTLIER) cc_final: -0.0156 (tpp) REVERT: B 12 ILE cc_start: 0.3112 (OUTLIER) cc_final: 0.2824 (pt) REVERT: B 141 VAL cc_start: 0.7786 (t) cc_final: 0.7577 (m) REVERT: B 345 SER cc_start: 0.5588 (t) cc_final: 0.5143 (m) REVERT: F 1 MET cc_start: 0.3544 (mmm) cc_final: 0.3160 (mmm) REVERT: F 14 PHE cc_start: 0.5382 (m-80) cc_final: 0.4759 (m-80) REVERT: F 223 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.7155 (mm) REVERT: I 35 ASP cc_start: 0.6440 (OUTLIER) cc_final: 0.5710 (t70) REVERT: I 336 MET cc_start: 0.4695 (mpt) cc_final: 0.4288 (mpt) REVERT: M 17 PHE cc_start: 0.2589 (t80) cc_final: 0.2300 (t80) REVERT: N 19 LYS cc_start: 0.7106 (mtpm) cc_final: 0.6534 (mptp) REVERT: N 205 GLN cc_start: 0.6019 (mm-40) cc_final: 0.5519 (mp10) outliers start: 41 outliers final: 12 residues processed: 289 average time/residue: 0.5573 time to fit residues: 196.9021 Evaluate side-chains 251 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 235 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 12 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain L residue 219 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 65 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 288 optimal weight: 9.9990 chunk 291 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 218 optimal weight: 0.7980 chunk 328 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN B 360 HIS B 430 GLN F 34 ASN F 66 ASN F 129 ASN F 205 GLN F 207 HIS ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 414 ASN L 349 GLN 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 329 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5391 r_free = 0.5391 target = 0.286609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5093 r_free = 0.5093 target = 0.250655 restraints weight = 46964.766| |-----------------------------------------------------------------------------| r_work (start): 0.5054 rms_B_bonded: 2.95 r_work: 0.4895 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4696 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 32375 Z= 0.274 Angle : 0.819 26.886 44449 Z= 0.433 Chirality : 0.050 0.245 4901 Planarity : 0.006 0.077 5060 Dihedral : 18.855 179.587 5854 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.67 % Favored : 93.30 % Rotamer: Outliers : 2.58 % Allowed : 10.19 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.14), residues: 3386 helix: 0.51 (0.15), residues: 1101 sheet: -0.73 (0.21), residues: 612 loop : -2.07 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 481 TYR 0.030 0.002 TYR L 505 PHE 0.050 0.003 PHE I 120 TRP 0.056 0.003 TRP E 20 HIS 0.010 0.002 HIS L 217 Details of bonding type rmsd covalent geometry : bond 0.00603 (32370) covalent geometry : angle 0.81860 (44449) hydrogen bonds : bond 0.06346 ( 1195) hydrogen bonds : angle 5.79551 ( 3388) Misc. bond : bond 0.00753 ( 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 365 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 286 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.2363 (OUTLIER) cc_final: 0.1773 (ttmt) REVERT: A 276 ARG cc_start: -0.0910 (OUTLIER) cc_final: -0.1691 (mmp80) REVERT: A 277 MET cc_start: -0.1566 (mmm) cc_final: -0.2192 (mmm) REVERT: A 279 ASP cc_start: 0.0795 (OUTLIER) cc_final: 0.0514 (t0) REVERT: A 392 TYR cc_start: 0.6350 (OUTLIER) cc_final: 0.5706 (p90) REVERT: A 395 MET cc_start: 0.2612 (OUTLIER) cc_final: -0.0068 (tmt) REVERT: B 25 ASP cc_start: 0.5210 (m-30) cc_final: 0.4920 (t0) REVERT: B 341 GLN cc_start: 0.5285 (OUTLIER) cc_final: 0.4991 (pt0) REVERT: B 356 GLU cc_start: 0.5695 (tm-30) cc_final: 0.5407 (tm-30) REVERT: F 1 MET cc_start: 0.3621 (mmm) cc_final: 0.3161 (mmm) REVERT: F 14 PHE cc_start: 0.6119 (m-80) cc_final: 0.5051 (m-80) REVERT: F 86 TRP cc_start: 0.5318 (t60) cc_final: 0.4988 (t60) REVERT: F 88 SER cc_start: 0.5926 (p) cc_final: 0.5689 (p) REVERT: F 364 ARG cc_start: 0.5523 (OUTLIER) cc_final: 0.4033 (mmm-85) REVERT: I 336 MET cc_start: 0.5294 (mpt) cc_final: 0.4831 (mpt) REVERT: L 14 PHE cc_start: 0.6163 (m-80) cc_final: 0.5620 (m-80) REVERT: L 219 ILE cc_start: 0.7183 (OUTLIER) cc_final: 0.6785 (mp) REVERT: N 19 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.6651 (mmtp) REVERT: N 60 ILE cc_start: 0.6878 (pp) cc_final: 0.6542 (mt) REVERT: N 256 ILE cc_start: 0.5466 (OUTLIER) cc_final: 0.5147 (tt) REVERT: N 497 LYS cc_start: 0.8071 (mptt) cc_final: 0.7857 (mptt) outliers start: 79 outliers final: 31 residues processed: 344 average time/residue: 0.5267 time to fit residues: 224.9202 Evaluate side-chains 284 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 243 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 276 ARG Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 392 TYR 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 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 341 GLN Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 407 ARG 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 78 LEU Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 113 VAL 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 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 N residue 19 LYS Chi-restraints excluded: chain N residue 256 ILE Chi-restraints excluded: chain N residue 452 ILE Chi-restraints excluded: chain N residue 504 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 301 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 289 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 278 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 318 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN F 129 ASN F 207 HIS F 296 ASN F 325 ASN I 254 ASN L 349 GLN M 370 ASN ** N 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 329 HIS N 341 GLN N 446 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5383 r_free = 0.5383 target = 0.285790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5094 r_free = 0.5094 target = 0.250554 restraints weight = 46715.148| |-----------------------------------------------------------------------------| r_work (start): 0.5056 rms_B_bonded: 2.86 r_work: 0.4897 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4708 moved from start: 0.5932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 32375 Z= 0.210 Angle : 0.706 25.107 44449 Z= 0.369 Chirality : 0.046 0.332 4901 Planarity : 0.005 0.067 5060 Dihedral : 18.665 178.239 5854 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.45 % Allowed : 12.87 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.14), residues: 3386 helix: 0.61 (0.15), residues: 1126 sheet: -0.76 (0.21), residues: 609 loop : -2.05 (0.14), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 113 TYR 0.021 0.002 TYR N 65 PHE 0.029 0.002 PHE E 120 TRP 0.033 0.002 TRP A 20 HIS 0.007 0.001 HIS L 217 Details of bonding type rmsd covalent geometry : bond 0.00468 (32370) covalent geometry : angle 0.70589 (44449) hydrogen bonds : bond 0.05041 ( 1195) hydrogen bonds : angle 5.45961 ( 3388) Misc. bond : bond 0.00644 ( 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 342 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 267 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: -0.1395 (mmm) cc_final: -0.2206 (mmm) REVERT: A 279 ASP cc_start: 0.0808 (t0) cc_final: 0.0479 (t0) REVERT: A 392 TYR cc_start: 0.6234 (OUTLIER) cc_final: 0.5906 (p90) REVERT: A 395 MET cc_start: 0.2500 (OUTLIER) cc_final: -0.0191 (tmt) REVERT: B 132 GLU cc_start: 0.5729 (mt-10) cc_final: 0.5453 (mt-10) REVERT: B 370 TRP cc_start: 0.3666 (t-100) cc_final: 0.3247 (t-100) REVERT: E 20 TRP cc_start: 0.6251 (t60) cc_final: 0.5920 (t60) REVERT: F 1 MET cc_start: 0.3500 (mmm) cc_final: 0.2974 (mmm) REVERT: F 14 PHE cc_start: 0.5926 (m-80) cc_final: 0.4304 (m-80) REVERT: F 86 TRP cc_start: 0.5504 (t60) cc_final: 0.5118 (t60) REVERT: F 219 ILE cc_start: 0.6473 (OUTLIER) cc_final: 0.6189 (mp) REVERT: F 283 LEU cc_start: 0.4617 (OUTLIER) cc_final: 0.4274 (tp) REVERT: I 135 PHE cc_start: 0.6241 (m-10) cc_final: 0.5810 (m-10) REVERT: I 336 MET cc_start: 0.5365 (mpt) cc_final: 0.4781 (mpt) REVERT: L 14 PHE cc_start: 0.6216 (m-80) cc_final: 0.5760 (m-80) REVERT: L 139 TRP cc_start: 0.6183 (m100) cc_final: 0.5252 (t-100) REVERT: L 419 PHE cc_start: 0.4446 (m-80) cc_final: 0.4102 (m-80) REVERT: N 19 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6721 (mptt) REVERT: N 365 PHE cc_start: 0.0583 (OUTLIER) cc_final: -0.2784 (m-80) REVERT: N 370 TRP cc_start: 0.3123 (t-100) cc_final: 0.2857 (t-100) REVERT: N 443 ILE cc_start: 0.1155 (OUTLIER) cc_final: 0.0144 (mt) REVERT: N 497 LYS cc_start: 0.8049 (mptt) cc_final: 0.7806 (mptt) outliers start: 75 outliers final: 36 residues processed: 321 average time/residue: 0.4516 time to fit residues: 179.5810 Evaluate side-chains 289 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 246 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 43 VAL 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 454 GLN Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 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 104 SER Chi-restraints excluded: chain I residue 107 ASP Chi-restraints excluded: chain L residue 447 LYS 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 M residue 265 ILE Chi-restraints excluded: chain N residue 19 LYS Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 256 ILE Chi-restraints excluded: chain N residue 365 PHE Chi-restraints excluded: chain N residue 443 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 294 optimal weight: 0.9990 chunk 201 optimal weight: 0.0070 chunk 251 optimal weight: 0.8980 chunk 248 optimal weight: 0.5980 chunk 185 optimal weight: 0.9990 chunk 244 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 360 HIS ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 251 HIS ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN M 370 ASN N 439 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5394 r_free = 0.5394 target = 0.287321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5114 r_free = 0.5114 target = 0.252767 restraints weight = 47137.526| |-----------------------------------------------------------------------------| r_work (start): 0.5080 rms_B_bonded: 2.86 r_work: 0.4917 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4656 moved from start: 0.6225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 32375 Z= 0.153 Angle : 0.642 21.937 44449 Z= 0.334 Chirality : 0.043 0.191 4901 Planarity : 0.005 0.058 5060 Dihedral : 18.460 177.735 5854 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.19 % Allowed : 14.28 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.14), residues: 3386 helix: 0.92 (0.16), residues: 1132 sheet: -0.63 (0.21), residues: 631 loop : -1.98 (0.14), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 54 TYR 0.022 0.001 TYR B 6 PHE 0.031 0.002 PHE I 120 TRP 0.058 0.002 TRP A 20 HIS 0.003 0.001 HIS L 207 Details of bonding type rmsd covalent geometry : bond 0.00336 (32370) covalent geometry : angle 0.64228 (44449) hydrogen bonds : bond 0.04279 ( 1195) hydrogen bonds : angle 5.09810 ( 3388) Misc. bond : bond 0.00744 ( 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 314 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 247 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.2648 (OUTLIER) cc_final: 0.2423 (mtmt) REVERT: A 277 MET cc_start: -0.1403 (mmm) cc_final: -0.2492 (mmm) REVERT: A 392 TYR cc_start: 0.6416 (OUTLIER) cc_final: 0.5855 (p90) REVERT: A 395 MET cc_start: 0.2412 (OUTLIER) cc_final: -0.0267 (tmt) REVERT: B 132 GLU cc_start: 0.5649 (mt-10) cc_final: 0.5425 (mt-10) REVERT: B 327 GLN cc_start: 0.4985 (OUTLIER) cc_final: 0.3961 (mp10) REVERT: B 341 GLN cc_start: 0.5504 (OUTLIER) cc_final: 0.5024 (pt0) REVERT: B 370 TRP cc_start: 0.3316 (t-100) cc_final: 0.2227 (t-100) REVERT: E 87 GLN cc_start: 0.7610 (tp40) cc_final: 0.7370 (tp40) REVERT: F 1 MET cc_start: 0.3483 (mmm) cc_final: 0.2980 (mmm) REVERT: F 14 PHE cc_start: 0.5652 (m-80) cc_final: 0.4280 (m-80) REVERT: F 86 TRP cc_start: 0.5432 (t60) cc_final: 0.4895 (t60) REVERT: F 283 LEU cc_start: 0.4866 (OUTLIER) cc_final: 0.4503 (tp) REVERT: F 435 MET cc_start: 0.1211 (mtt) cc_final: 0.0868 (mtt) REVERT: I 323 ILE cc_start: 0.7066 (pt) cc_final: 0.6849 (mt) REVERT: I 336 MET cc_start: 0.5340 (mpt) cc_final: 0.4743 (mpt) REVERT: I 370 ASN cc_start: 0.4613 (OUTLIER) cc_final: 0.4240 (t0) REVERT: L 1 MET cc_start: 0.5843 (OUTLIER) cc_final: 0.5638 (tpp) REVERT: L 139 TRP cc_start: 0.6241 (m100) cc_final: 0.5235 (t-100) REVERT: L 419 PHE cc_start: 0.4315 (m-80) cc_final: 0.3935 (m-80) REVERT: M 21 LEU cc_start: 0.2925 (mt) cc_final: 0.1805 (tp) REVERT: N 19 LYS cc_start: 0.7304 (OUTLIER) cc_final: 0.6678 (mptt) REVERT: N 370 TRP cc_start: 0.3046 (t-100) cc_final: 0.2744 (t-100) REVERT: N 497 LYS cc_start: 0.7973 (mptt) cc_final: 0.7743 (mptt) outliers start: 67 outliers final: 28 residues processed: 296 average time/residue: 0.5132 time to fit residues: 189.6336 Evaluate side-chains 279 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 242 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 378 LEU Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 327 GLN 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 F residue 44 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 136 VAL 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 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 370 ASN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 384 VAL 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 33 TRP Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 265 ILE Chi-restraints excluded: chain M residue 370 ASN Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 19 LYS Chi-restraints excluded: chain N residue 74 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 207 optimal weight: 0.9990 chunk 232 optimal weight: 0.8980 chunk 222 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 264 optimal weight: 0.7980 chunk 251 optimal weight: 1.9990 chunk 347 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 244 optimal weight: 0.8980 chunk 302 optimal weight: 0.7980 chunk 146 optimal weight: 0.0060 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 405 ASN L 327 GLN L 329 HIS ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 370 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5388 r_free = 0.5388 target = 0.286501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5104 r_free = 0.5104 target = 0.251689 restraints weight = 46628.907| |-----------------------------------------------------------------------------| r_work (start): 0.5069 rms_B_bonded: 2.91 r_work: 0.4906 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4692 moved from start: 0.6582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 32375 Z= 0.158 Angle : 0.640 21.738 44449 Z= 0.331 Chirality : 0.043 0.198 4901 Planarity : 0.004 0.057 5060 Dihedral : 18.354 178.331 5854 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.45 % Allowed : 15.03 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.14), residues: 3386 helix: 0.94 (0.16), residues: 1134 sheet: -0.41 (0.22), residues: 602 loop : -2.00 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 19 TYR 0.027 0.001 TYR B 6 PHE 0.030 0.002 PHE I 120 TRP 0.078 0.002 TRP A 20 HIS 0.005 0.001 HIS L 207 Details of bonding type rmsd covalent geometry : bond 0.00348 (32370) covalent geometry : angle 0.64038 (44449) hydrogen bonds : bond 0.04319 ( 1195) hydrogen bonds : angle 5.06404 ( 3388) Misc. bond : bond 0.00551 ( 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 314 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 239 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.2808 (OUTLIER) cc_final: 0.2468 (mtmt) REVERT: A 277 MET cc_start: -0.1231 (mmm) cc_final: -0.2174 (mmm) REVERT: A 392 TYR cc_start: 0.6445 (OUTLIER) cc_final: 0.5897 (p90) REVERT: A 395 MET cc_start: 0.2108 (OUTLIER) cc_final: -0.0407 (tmt) REVERT: B 6 TYR cc_start: 0.5026 (t80) cc_final: 0.4771 (t80) REVERT: B 327 GLN cc_start: 0.4983 (OUTLIER) cc_final: 0.3955 (mp10) REVERT: B 356 GLU cc_start: 0.5701 (tm-30) cc_final: 0.5377 (tm-30) REVERT: B 370 TRP cc_start: 0.3631 (t-100) cc_final: 0.2308 (t-100) REVERT: E 405 ASN cc_start: 0.0965 (OUTLIER) cc_final: 0.0760 (p0) REVERT: F 1 MET cc_start: 0.3501 (mmm) cc_final: 0.2990 (mmm) REVERT: F 14 PHE cc_start: 0.5645 (m-80) cc_final: 0.4486 (m-80) REVERT: F 60 ILE cc_start: 0.7797 (pp) cc_final: 0.7545 (pp) REVERT: F 86 TRP cc_start: 0.5425 (t60) cc_final: 0.4891 (t60) REVERT: F 283 LEU cc_start: 0.4926 (OUTLIER) cc_final: 0.4588 (tp) REVERT: F 435 MET cc_start: 0.1191 (mtt) cc_final: 0.0898 (mtt) REVERT: I 135 PHE cc_start: 0.6194 (m-10) cc_final: 0.5830 (m-10) REVERT: I 323 ILE cc_start: 0.7140 (pt) cc_final: 0.6868 (mt) REVERT: I 336 MET cc_start: 0.5416 (mpt) cc_final: 0.4886 (mpt) REVERT: I 370 ASN cc_start: 0.4601 (OUTLIER) cc_final: 0.4242 (t0) REVERT: N 19 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.6742 (mptt) REVERT: N 365 PHE cc_start: 0.0374 (OUTLIER) cc_final: -0.2909 (m-80) REVERT: N 369 GLU cc_start: 0.4152 (tt0) cc_final: 0.3890 (mt-10) REVERT: N 370 TRP cc_start: 0.3005 (t-100) cc_final: 0.2688 (t-100) REVERT: N 497 LYS cc_start: 0.8015 (mptt) cc_final: 0.7811 (mptt) outliers start: 75 outliers final: 40 residues processed: 300 average time/residue: 0.5190 time to fit residues: 194.6939 Evaluate side-chains 283 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 234 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 335 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 392 TYR 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 129 ASN Chi-restraints excluded: chain B residue 327 GLN 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 61 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 405 ASN Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 223 ILE 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 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 78 LEU Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 370 ASN 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 460 LEU 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 43 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 19 LYS Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 365 PHE 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 107 optimal weight: 3.9990 chunk 237 optimal weight: 9.9990 chunk 80 optimal weight: 0.3980 chunk 301 optimal weight: 0.0770 chunk 20 optimal weight: 3.9990 chunk 258 optimal weight: 0.9980 chunk 228 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 296 optimal weight: 8.9990 chunk 318 optimal weight: 8.9990 chunk 315 optimal weight: 0.2980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 ASN I 254 ASN ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 205 GLN ** 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 = 0.5369 r_free = 0.5369 target = 0.284088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5099 r_free = 0.5099 target = 0.250644 restraints weight = 46675.095| |-----------------------------------------------------------------------------| r_work (start): 0.5060 rms_B_bonded: 2.59 r_work: 0.4900 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4719 moved from start: 0.7103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 32375 Z= 0.189 Angle : 0.689 24.792 44449 Z= 0.355 Chirality : 0.044 0.191 4901 Planarity : 0.005 0.061 5060 Dihedral : 18.380 177.937 5854 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.42 % Allowed : 15.94 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.14), residues: 3386 helix: 0.80 (0.16), residues: 1123 sheet: -0.49 (0.22), residues: 596 loop : -2.09 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 19 TYR 0.024 0.002 TYR B 6 PHE 0.033 0.002 PHE I 120 TRP 0.100 0.003 TRP A 20 HIS 0.007 0.001 HIS L 217 Details of bonding type rmsd covalent geometry : bond 0.00421 (32370) covalent geometry : angle 0.68855 (44449) hydrogen bonds : bond 0.04783 ( 1195) hydrogen bonds : angle 5.28995 ( 3388) Misc. bond : bond 0.00588 ( 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 318 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 244 time to evaluate : 1.338 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: -0.1381 (mmm) cc_final: -0.2552 (mmm) REVERT: A 392 TYR cc_start: 0.6418 (OUTLIER) cc_final: 0.6206 (p90) REVERT: A 395 MET cc_start: 0.2043 (OUTLIER) cc_final: -0.0673 (tmt) REVERT: B 1 MET cc_start: 0.2487 (mmp) cc_final: 0.2192 (mmp) REVERT: B 341 GLN cc_start: 0.5506 (OUTLIER) cc_final: 0.4942 (pt0) REVERT: B 370 TRP cc_start: 0.3935 (t-100) cc_final: 0.2556 (t-100) REVERT: E 36 ILE cc_start: 0.6077 (OUTLIER) cc_final: 0.5823 (pt) REVERT: F 1 MET cc_start: 0.3583 (mmm) cc_final: 0.3061 (mmm) REVERT: F 14 PHE cc_start: 0.5802 (m-80) cc_final: 0.4612 (m-80) REVERT: F 33 LEU cc_start: 0.7154 (tt) cc_final: 0.6923 (tt) REVERT: F 60 ILE cc_start: 0.7875 (pp) cc_final: 0.7633 (pp) REVERT: F 86 TRP cc_start: 0.5785 (t60) cc_final: 0.4810 (t60) REVERT: F 435 MET cc_start: 0.1285 (mtt) cc_final: 0.1018 (mtt) REVERT: I 261 CYS cc_start: 0.6894 (t) cc_final: 0.6615 (p) REVERT: I 323 ILE cc_start: 0.7293 (pt) cc_final: 0.6934 (mt) REVERT: I 336 MET cc_start: 0.5500 (mpt) cc_final: 0.5025 (mpt) REVERT: I 370 ASN cc_start: 0.4593 (OUTLIER) cc_final: 0.4326 (t0) REVERT: L 447 LYS cc_start: 0.5447 (OUTLIER) cc_final: 0.4622 (tmmt) REVERT: M 15 ASN cc_start: 0.1514 (OUTLIER) cc_final: 0.0969 (m-40) REVERT: N 19 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.6654 (mptt) REVERT: N 205 GLN cc_start: 0.6743 (mm-40) cc_final: 0.6246 (mm-40) REVERT: N 365 PHE cc_start: 0.0551 (OUTLIER) cc_final: -0.2854 (m-80) REVERT: N 369 GLU cc_start: 0.4086 (tt0) cc_final: 0.3883 (mt-10) REVERT: N 370 TRP cc_start: 0.3150 (t-100) cc_final: 0.2872 (t-100) outliers start: 74 outliers final: 42 residues processed: 304 average time/residue: 0.5250 time to fit residues: 199.4123 Evaluate side-chains 284 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 233 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 392 TYR 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 360 HIS 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 36 ILE Chi-restraints excluded: chain E residue 61 LEU 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 341 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 136 VAL 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 78 LEU Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 108 ILE 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 435 MET 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 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 65 SER Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 19 LYS Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 365 PHE 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 50 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 197 optimal weight: 3.9990 chunk 267 optimal weight: 0.0060 chunk 312 optimal weight: 0.8980 chunk 208 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 287 optimal weight: 0.6980 chunk 255 optimal weight: 0.8980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 325 ASN ** 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 = 0.5377 r_free = 0.5377 target = 0.285847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5098 r_free = 0.5098 target = 0.251655 restraints weight = 46622.026| |-----------------------------------------------------------------------------| r_work (start): 0.5075 rms_B_bonded: 2.75 r_work: 0.4912 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4696 moved from start: 0.7305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 32375 Z= 0.152 Angle : 0.644 21.739 44449 Z= 0.330 Chirality : 0.042 0.195 4901 Planarity : 0.004 0.056 5060 Dihedral : 18.274 178.546 5854 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.09 % Allowed : 16.99 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.14), residues: 3386 helix: 0.94 (0.16), residues: 1129 sheet: -0.68 (0.21), residues: 642 loop : -2.03 (0.14), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 19 TYR 0.032 0.001 TYR B 6 PHE 0.030 0.002 PHE I 120 TRP 0.102 0.002 TRP A 20 HIS 0.005 0.001 HIS L 207 Details of bonding type rmsd covalent geometry : bond 0.00337 (32370) covalent geometry : angle 0.64432 (44449) hydrogen bonds : bond 0.04190 ( 1195) hydrogen bonds : angle 5.05860 ( 3388) Misc. bond : bond 0.00510 ( 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 304 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 240 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: -0.1252 (mmm) cc_final: -0.2450 (mmm) REVERT: A 395 MET cc_start: 0.2066 (OUTLIER) cc_final: -0.0681 (tmt) REVERT: B 1 MET cc_start: 0.2388 (mmp) cc_final: 0.2079 (mmp) REVERT: B 25 ASP cc_start: 0.5332 (m-30) cc_final: 0.5002 (m-30) REVERT: B 370 TRP cc_start: 0.3823 (t-100) cc_final: 0.2758 (t-100) REVERT: E 36 ILE cc_start: 0.6079 (OUTLIER) cc_final: 0.5761 (pt) REVERT: F 1 MET cc_start: 0.3565 (mmm) cc_final: 0.2974 (mmm) REVERT: F 14 PHE cc_start: 0.5689 (m-80) cc_final: 0.4616 (m-80) REVERT: F 33 LEU cc_start: 0.7087 (tt) cc_final: 0.6866 (tt) REVERT: F 60 ILE cc_start: 0.7768 (pp) cc_final: 0.7530 (pp) REVERT: F 86 TRP cc_start: 0.5634 (t60) cc_final: 0.4641 (t60) REVERT: F 296 ASN cc_start: 0.6077 (OUTLIER) cc_final: 0.4945 (m110) REVERT: F 435 MET cc_start: 0.1383 (mtt) cc_final: 0.1104 (mtt) REVERT: F 497 LYS cc_start: 0.6771 (ptmm) cc_final: 0.6483 (ttpp) REVERT: I 261 CYS cc_start: 0.6953 (t) cc_final: 0.6650 (p) REVERT: I 323 ILE cc_start: 0.7131 (pt) cc_final: 0.6772 (mt) REVERT: I 336 MET cc_start: 0.5441 (mpt) cc_final: 0.4989 (mpt) REVERT: I 370 ASN cc_start: 0.4477 (OUTLIER) cc_final: 0.4218 (t0) REVERT: L 460 LEU cc_start: 0.6305 (OUTLIER) cc_final: 0.5753 (tt) REVERT: N 19 LYS cc_start: 0.7272 (OUTLIER) cc_final: 0.6676 (mptt) REVERT: N 205 GLN cc_start: 0.6734 (mm-40) cc_final: 0.6278 (mm-40) REVERT: N 365 PHE cc_start: 0.0494 (OUTLIER) cc_final: -0.2909 (m-80) REVERT: N 369 GLU cc_start: 0.4484 (tt0) cc_final: 0.3991 (mt-10) REVERT: N 370 TRP cc_start: 0.3179 (t-100) cc_final: 0.2896 (t-100) outliers start: 64 outliers final: 42 residues processed: 289 average time/residue: 0.5469 time to fit residues: 196.2973 Evaluate side-chains 279 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 230 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 378 LEU 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 360 HIS 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 36 ILE 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 274 GLU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 296 ASN 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 78 LEU Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 327 SER Chi-restraints excluded: chain I residue 370 ASN 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 33 TRP Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 19 LYS Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 365 PHE Chi-restraints excluded: chain N residue 377 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 148 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 198 optimal weight: 5.9990 chunk 265 optimal weight: 3.9990 chunk 211 optimal weight: 0.2980 chunk 195 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 193 optimal weight: 0.0040 chunk 210 optimal weight: 5.9990 chunk 274 optimal weight: 0.0980 overall best weight: 0.3392 ------------------------------------------------------------------------------- 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 L 35 ASN L 327 GLN L 329 HIS ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 329 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5399 r_free = 0.5399 target = 0.288686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5123 r_free = 0.5123 target = 0.254401 restraints weight = 46746.378| |-----------------------------------------------------------------------------| r_work (start): 0.5097 rms_B_bonded: 2.80 r_work: 0.4940 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4615 moved from start: 0.7399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 32375 Z= 0.124 Angle : 0.615 17.854 44449 Z= 0.314 Chirality : 0.041 0.198 4901 Planarity : 0.004 0.052 5060 Dihedral : 18.162 179.558 5854 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.40 % Allowed : 18.23 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.14), residues: 3386 helix: 1.17 (0.16), residues: 1135 sheet: -0.50 (0.21), residues: 638 loop : -1.92 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 19 TYR 0.032 0.001 TYR B 6 PHE 0.027 0.001 PHE I 120 TRP 0.102 0.002 TRP A 20 HIS 0.004 0.001 HIS L 217 Details of bonding type rmsd covalent geometry : bond 0.00271 (32370) covalent geometry : angle 0.61533 (44449) hydrogen bonds : bond 0.03659 ( 1195) hydrogen bonds : angle 4.81119 ( 3388) Misc. bond : bond 0.00456 ( 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 281 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 238 time to evaluate : 1.140 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: -0.1446 (mmm) cc_final: -0.2580 (mmm) REVERT: A 395 MET cc_start: 0.1912 (OUTLIER) cc_final: -0.0746 (tmt) REVERT: B 1 MET cc_start: 0.2235 (mmp) cc_final: 0.2013 (mmp) REVERT: B 25 ASP cc_start: 0.5283 (m-30) cc_final: 0.5013 (m-30) REVERT: B 370 TRP cc_start: 0.3623 (t-100) cc_final: 0.2928 (t-100) REVERT: E 17 PHE cc_start: 0.5559 (t80) cc_final: 0.4629 (t80) REVERT: F 1 MET cc_start: 0.3569 (mmm) cc_final: 0.3039 (mmm) REVERT: F 14 PHE cc_start: 0.5390 (m-80) cc_final: 0.4406 (m-80) REVERT: F 33 LEU cc_start: 0.7039 (tt) cc_final: 0.6827 (tt) REVERT: F 60 ILE cc_start: 0.7731 (pp) cc_final: 0.7500 (pp) REVERT: F 86 TRP cc_start: 0.5539 (t60) cc_final: 0.4635 (t60) REVERT: F 219 ILE cc_start: 0.6449 (OUTLIER) cc_final: 0.6183 (mp) REVERT: F 296 ASN cc_start: 0.5955 (OUTLIER) cc_final: 0.4768 (m110) REVERT: F 364 ARG cc_start: 0.5493 (OUTLIER) cc_final: 0.4603 (ppt170) REVERT: F 435 MET cc_start: 0.1221 (mtt) cc_final: 0.0963 (mtt) REVERT: F 497 LYS cc_start: 0.6810 (ptmm) cc_final: 0.6596 (ttpp) REVERT: I 261 CYS cc_start: 0.6913 (t) cc_final: 0.6568 (p) REVERT: I 323 ILE cc_start: 0.7026 (pt) cc_final: 0.6726 (mt) REVERT: I 327 SER cc_start: 0.7615 (OUTLIER) cc_final: 0.7193 (p) REVERT: I 336 MET cc_start: 0.5304 (mpt) cc_final: 0.4816 (mpt) REVERT: I 370 ASN cc_start: 0.4373 (OUTLIER) cc_final: 0.4097 (t0) REVERT: L 460 LEU cc_start: 0.6080 (OUTLIER) cc_final: 0.5653 (tt) REVERT: M 5 ILE cc_start: 0.7624 (mt) cc_final: 0.7345 (pt) REVERT: N 19 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6662 (mptt) REVERT: N 205 GLN cc_start: 0.6559 (mm-40) cc_final: 0.6233 (mm-40) REVERT: N 369 GLU cc_start: 0.4462 (tt0) cc_final: 0.3979 (mt-10) REVERT: N 370 TRP cc_start: 0.3017 (t-100) cc_final: 0.2571 (t-100) outliers start: 43 outliers final: 24 residues processed: 271 average time/residue: 0.5703 time to fit residues: 190.6705 Evaluate side-chains 262 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 230 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 378 LEU Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 296 ASN 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 465 LEU Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 327 SER Chi-restraints excluded: chain I residue 370 ASN Chi-restraints excluded: chain L residue 435 MET Chi-restraints excluded: chain L residue 460 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain M residue 43 VAL 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 429 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 100 optimal weight: 0.8980 chunk 286 optimal weight: 0.9990 chunk 259 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 273 optimal weight: 0.5980 chunk 341 optimal weight: 2.9990 chunk 291 optimal weight: 0.9980 chunk 306 optimal weight: 2.9990 chunk 311 optimal weight: 0.6980 chunk 97 optimal weight: 0.0060 chunk 14 optimal weight: 4.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 ASN F 16 HIS F 325 ASN ** 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 = 0.5388 r_free = 0.5388 target = 0.287005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5121 r_free = 0.5121 target = 0.253445 restraints weight = 46701.870| |-----------------------------------------------------------------------------| r_work (start): 0.5093 rms_B_bonded: 2.54 r_work: 0.4930 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4645 moved from start: 0.7592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 32375 Z= 0.145 Angle : 0.643 19.468 44449 Z= 0.328 Chirality : 0.042 0.196 4901 Planarity : 0.004 0.057 5060 Dihedral : 18.153 179.690 5854 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.44 % Allowed : 18.56 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.14), residues: 3386 helix: 1.15 (0.16), residues: 1133 sheet: -0.53 (0.21), residues: 638 loop : -1.92 (0.14), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 54 TYR 0.017 0.001 TYR B 321 PHE 0.032 0.002 PHE L 210 TRP 0.106 0.002 TRP A 20 HIS 0.005 0.001 HIS L 217 Details of bonding type rmsd covalent geometry : bond 0.00323 (32370) covalent geometry : angle 0.64260 (44449) hydrogen bonds : bond 0.03993 ( 1195) hydrogen bonds : angle 4.89050 ( 3388) Misc. bond : bond 0.00498 ( 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 277 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 233 time to evaluate : 1.126 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 202 GLU cc_start: 0.5503 (OUTLIER) cc_final: 0.5052 (pm20) REVERT: A 277 MET cc_start: -0.1193 (mmm) cc_final: -0.2361 (mmm) REVERT: A 395 MET cc_start: 0.1736 (OUTLIER) cc_final: -0.0889 (tmt) REVERT: B 25 ASP cc_start: 0.5277 (m-30) cc_final: 0.4962 (m-30) REVERT: B 370 TRP cc_start: 0.3801 (t-100) cc_final: 0.2990 (t-100) REVERT: E 17 PHE cc_start: 0.5580 (t80) cc_final: 0.4683 (t80) REVERT: F 1 MET cc_start: 0.3816 (mmm) cc_final: 0.3322 (mmm) REVERT: F 14 PHE cc_start: 0.5641 (m-80) cc_final: 0.4657 (m-80) REVERT: F 33 LEU cc_start: 0.7187 (tt) cc_final: 0.6987 (tt) REVERT: F 60 ILE cc_start: 0.7763 (pp) cc_final: 0.7528 (pp) REVERT: F 79 GLU cc_start: 0.4979 (pm20) cc_final: 0.4675 (mm-30) REVERT: F 86 TRP cc_start: 0.5666 (t60) cc_final: 0.4615 (t60) REVERT: F 435 MET cc_start: 0.1436 (mtt) cc_final: 0.1170 (mtt) REVERT: I 99 ILE cc_start: 0.6420 (mm) cc_final: 0.6127 (mm) REVERT: I 261 CYS cc_start: 0.6886 (t) cc_final: 0.6593 (p) REVERT: I 323 ILE cc_start: 0.7173 (pt) cc_final: 0.6842 (mt) REVERT: I 336 MET cc_start: 0.5343 (mpt) cc_final: 0.4889 (mpt) REVERT: I 370 ASN cc_start: 0.4430 (OUTLIER) cc_final: 0.4156 (t0) REVERT: L 460 LEU cc_start: 0.6187 (OUTLIER) cc_final: 0.5711 (tt) REVERT: N 19 LYS cc_start: 0.7231 (OUTLIER) cc_final: 0.6600 (mptt) REVERT: N 205 GLN cc_start: 0.6651 (mm-40) cc_final: 0.6341 (mm-40) REVERT: N 369 GLU cc_start: 0.4501 (tt0) cc_final: 0.4108 (mt-10) REVERT: N 370 TRP cc_start: 0.3075 (t-100) cc_final: 0.2310 (t-100) outliers start: 44 outliers final: 27 residues processed: 267 average time/residue: 0.5448 time to fit residues: 180.0484 Evaluate side-chains 260 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 74 MET Chi-restraints excluded: chain B residue 360 HIS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 136 VAL 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 465 LEU Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 370 ASN Chi-restraints excluded: chain L residue 384 VAL Chi-restraints excluded: chain L residue 435 MET Chi-restraints excluded: chain L residue 460 LEU 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 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 429 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 205 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 218 optimal weight: 0.4980 chunk 124 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 320 optimal weight: 0.9990 chunk 331 optimal weight: 0.6980 chunk 223 optimal weight: 7.9990 chunk 281 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 325 ASN ** 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 = 0.5373 r_free = 0.5373 target = 0.285009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5090 r_free = 0.5090 target = 0.250157 restraints weight = 46574.794| |-----------------------------------------------------------------------------| r_work (start): 0.5063 rms_B_bonded: 2.81 r_work: 0.4904 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4726 moved from start: 0.7953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 32375 Z= 0.170 Angle : 0.685 23.287 44449 Z= 0.350 Chirality : 0.044 0.223 4901 Planarity : 0.005 0.062 5060 Dihedral : 18.239 179.509 5854 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.63 % Allowed : 18.49 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.14), residues: 3386 helix: 1.06 (0.16), residues: 1117 sheet: -0.37 (0.22), residues: 594 loop : -2.00 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 19 TYR 0.016 0.001 TYR B 321 PHE 0.040 0.002 PHE A 17 TRP 0.108 0.002 TRP A 20 HIS 0.008 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00384 (32370) covalent geometry : angle 0.68486 (44449) hydrogen bonds : bond 0.04429 ( 1195) hydrogen bonds : angle 5.12206 ( 3388) Misc. bond : bond 0.00538 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11713.20 seconds wall clock time: 200 minutes 30.35 seconds (12030.35 seconds total)