Starting phenix.real_space_refine on Sun Aug 9 00:35:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8spo_40680/08_2026/8spo_40680_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8spo_40680/08_2026/8spo_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 { model { file = "/net/cci-nas-00/data/ceres_data/8spo_40680/08_2026/8spo_40680_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8spo_40680/08_2026/8spo_40680_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8spo_40680/08_2026/8spo_40680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8spo_40680/08_2026/8spo_40680.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: 6.59, per 1000 atoms: 0.21 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: 2.85 Conformation dependent library (CDL) restraints added in 1.2 seconds 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6522 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 42 sheets defined 36.3% alpha, 19.1% beta 33 base pairs and 117 stacking pairs defined. Time for finding SS restraints: 3.60 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: 6.47 Time building geometry restraints manager: 3.74 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: 43258 1.81 - 3.61: 1070 3.61 - 5.42: 105 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: 6.670 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: 0.040 Extract box with map and model: 0.610 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 30.220 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.100 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:7.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2988 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 : 0.007 0.671 32375 Z= 0.599 Angle : 0.635 9.028 44449 Z= 0.436 Chirality : 0.259 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 are 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/Z covalent geometry : bond 0.00384 / 0.26 (32370) covalent geometry : angle 0.63542 / 0.44 (44449) hydrogen bonds : bond 0.18460 / 12.21 ( 1195) hydrogen bonds : angle 7.16918 / 5.02 ( 3388) Misc. bond : bond 0.43189 / 21.72 ( 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 : 0.924 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: 0.6897 (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: 0.5694 time to fit residues: 213.6725 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 : 1.023 ------------------------------------------------------------------------------- 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: 10.0000 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... B 129 ASN B 217 HIS ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN F 18 GLN F 129 ASN F 329 HIS ** I 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 446 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5530 r_free = 0.5530 target = 0.306230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5291 r_free = 0.5291 target = 0.275860 restraints weight = 50202.801| |-----------------------------------------------------------------------------| r_work (start): 0.5278 rms_B_bonded: 2.81 r_work: 0.5164 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.5164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4129 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 32375 Z= 0.227 Angle : 0.774 18.214 44449 Z= 0.414 Chirality : 0.052 0.740 4901 Planarity : 0.006 0.074 5060 Dihedral : 19.044 179.036 5856 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.24 % Allowed : 6.50 % Favored : 92.26 % 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 are not related in a simple way. whole: -1.05 (0.14), residues: 3386 helix: 0.93 (0.16), residues: 1145 sheet: -0.77 (0.19), residues: 683 loop : -1.94 (0.14), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 276 TYR 0.028 0.002 TYR M 210 PHE 0.045 0.003 PHE B 503 TRP 0.019 0.002 TRP N 370 HIS 0.012 0.001 HIS I 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.23 (32370) covalent geometry : angle 0.77353 / 0.41 (44449) hydrogen bonds : bond 0.05527 / 3.57 ( 1195) hydrogen bonds : angle 5.43295 / 3.81 ( 3388) Misc. bond : bond 0.01470 / 0.76 ( 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 298 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 260 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: -0.1365 (mmm) cc_final: -0.2194 (mmm) REVERT: A 395 MET cc_start: 0.2464 (OUTLIER) cc_final: -0.0297 (tpp) REVERT: B 12 ILE cc_start: 0.3095 (OUTLIER) cc_final: 0.2784 (pt) REVERT: B 345 SER cc_start: 0.5878 (t) cc_final: 0.5377 (m) REVERT: E 274 GLU cc_start: 0.4242 (OUTLIER) cc_final: 0.3525 (mp0) REVERT: F 79 GLU cc_start: 0.4690 (tp30) cc_final: 0.3633 (mm-30) REVERT: F 254 TRP cc_start: 0.3955 (m100) cc_final: 0.3718 (m100) REVERT: I 35 ASP cc_start: 0.5844 (OUTLIER) cc_final: 0.5274 (t70) REVERT: I 336 MET cc_start: 0.4802 (mpt) cc_final: 0.4353 (mpt) REVERT: M 17 PHE cc_start: 0.2425 (t80) cc_final: 0.2036 (t80) REVERT: N 19 LYS cc_start: 0.7020 (mtpm) cc_final: 0.6515 (mptp) outliers start: 38 outliers final: 12 residues processed: 275 average time/residue: 0.5395 time to fit residues: 181.4943 Evaluate side-chains 254 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 238 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 274 GLU 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 M residue 5 ILE 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: 0.8980 chunk 17 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 288 optimal weight: 0.9980 chunk 291 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 328 optimal weight: 0.0070 chunk 113 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 ASN A 156 GLN B 129 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 HIS ** I 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 349 GLN ** L 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 446 ASN N 205 GLN ** N 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5476 r_free = 0.5476 target = 0.298013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.5209 r_free = 0.5209 target = 0.264396 restraints weight = 48781.184| |-----------------------------------------------------------------------------| r_work (start): 0.5181 rms_B_bonded: 2.87 r_work: 0.5042 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.5042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4451 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 32375 Z= 0.212 Angle : 0.697 16.697 44449 Z= 0.380 Chirality : 0.048 0.342 4901 Planarity : 0.005 0.059 5060 Dihedral : 18.733 179.692 5854 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.45 % Allowed : 9.34 % Favored : 88.21 % 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 are not related in a simple way. whole: -1.01 (0.14), residues: 3386 helix: 0.88 (0.15), residues: 1151 sheet: -0.52 (0.20), residues: 650 loop : -1.96 (0.14), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 481 TYR 0.030 0.002 TYR N 505 PHE 0.036 0.003 PHE A 17 TRP 0.031 0.003 TRP L 370 HIS 0.011 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 (32370) covalent geometry : angle 0.69747 / 0.38 (44449) hydrogen bonds : bond 0.05373 / 3.53 ( 1195) hydrogen bonds : angle 5.25823 / 3.66 ( 3388) Misc. bond : bond 0.01480 / 0.76 ( 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 332 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 257 time to evaluate : 1.083 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 156 GLN cc_start: 0.5687 (OUTLIER) cc_final: 0.5115 (mt0) REVERT: A 211 LYS cc_start: 0.2347 (OUTLIER) cc_final: 0.2144 (mtmt) REVERT: A 277 MET cc_start: -0.1709 (mmm) cc_final: -0.2230 (mmm) REVERT: A 279 ASP cc_start: 0.0362 (t70) cc_final: -0.0175 (t0) REVERT: A 395 MET cc_start: 0.2449 (OUTLIER) cc_final: -0.0029 (tpp) REVERT: B 6 TYR cc_start: 0.4560 (t80) cc_final: 0.4255 (t80) REVERT: B 21 THR cc_start: 0.7118 (t) cc_final: 0.6552 (m) REVERT: B 345 SER cc_start: 0.5696 (t) cc_final: 0.5181 (m) REVERT: E 271 LYS cc_start: 0.5917 (mmmt) cc_final: 0.5640 (mmmt) REVERT: E 274 GLU cc_start: 0.4131 (OUTLIER) cc_final: 0.3425 (mp0) REVERT: F 14 PHE cc_start: 0.5361 (m-80) cc_final: 0.4484 (m-80) REVERT: I 323 ILE cc_start: 0.6451 (OUTLIER) cc_final: 0.5908 (mt) REVERT: I 336 MET cc_start: 0.5054 (OUTLIER) cc_final: 0.4603 (mpt) outliers start: 75 outliers final: 25 residues processed: 305 average time/residue: 0.5333 time to fit residues: 202.1143 Evaluate side-chains 273 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 210 TYR Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 327 SER Chi-restraints excluded: chain I residue 336 MET Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 372 THR Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 205 GLN Chi-restraints excluded: chain N residue 299 CYS Chi-restraints excluded: chain N residue 377 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 301 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 289 optimal weight: 30.0000 chunk 40 optimal weight: 0.0980 chunk 44 optimal weight: 2.9990 chunk 192 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 278 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 318 optimal weight: 7.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 207 HIS ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN E 15 ASN F 414 ASN ** L 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 205 GLN ** N 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5466 r_free = 0.5466 target = 0.296232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5201 r_free = 0.5201 target = 0.262381 restraints weight = 48180.982| |-----------------------------------------------------------------------------| r_work (start): 0.5165 rms_B_bonded: 2.96 r_work: 0.5015 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.5015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4531 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 32375 Z= 0.179 Angle : 0.638 17.729 44449 Z= 0.350 Chirality : 0.046 0.340 4901 Planarity : 0.005 0.057 5060 Dihedral : 18.612 179.467 5854 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.25 % Allowed : 11.24 % Favored : 86.51 % 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 are not related in a simple way. whole: -0.91 (0.14), residues: 3386 helix: 0.99 (0.16), residues: 1142 sheet: -0.39 (0.20), residues: 652 loop : -1.95 (0.14), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 481 TYR 0.017 0.002 TYR N 65 PHE 0.031 0.002 PHE I 120 TRP 0.032 0.002 TRP F 86 HIS 0.008 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (32370) covalent geometry : angle 0.63780 / 0.35 (44449) hydrogen bonds : bond 0.04757 / 3.13 ( 1195) hydrogen bonds : angle 5.12059 / 3.57 ( 3388) Misc. bond : bond 0.00678 / 0.36 ( 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 314 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 245 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.2425 (OUTLIER) cc_final: 0.1665 (ttpt) REVERT: A 277 MET cc_start: -0.1621 (mmm) cc_final: -0.2121 (mmm) REVERT: A 395 MET cc_start: 0.2144 (OUTLIER) cc_final: -0.0078 (tpp) REVERT: B 141 VAL cc_start: 0.7808 (t) cc_final: 0.7607 (m) REVERT: E 274 GLU cc_start: 0.4115 (OUTLIER) cc_final: 0.3622 (mp0) REVERT: F 12 ILE cc_start: 0.2527 (OUTLIER) cc_final: 0.2293 (pt) REVERT: F 14 PHE cc_start: 0.5516 (m-80) cc_final: 0.4414 (m-80) REVERT: F 219 ILE cc_start: 0.6557 (OUTLIER) cc_final: 0.6277 (mp) REVERT: F 223 ILE cc_start: 0.7374 (OUTLIER) cc_final: 0.7050 (mm) REVERT: F 364 ARG cc_start: 0.5354 (OUTLIER) cc_final: 0.3950 (mmm-85) REVERT: F 407 ARG cc_start: 0.5686 (ttt180) cc_final: 0.5237 (ttt180) REVERT: I 323 ILE cc_start: 0.6670 (OUTLIER) cc_final: 0.6192 (mt) REVERT: I 336 MET cc_start: 0.5165 (mpt) cc_final: 0.4650 (mpt) REVERT: N 443 ILE cc_start: 0.0237 (OUTLIER) cc_final: -0.1097 (mt) outliers start: 69 outliers final: 27 residues processed: 295 average time/residue: 0.5283 time to fit residues: 193.2228 Evaluate side-chains 270 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 364 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 43 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 210 TYR Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 327 SER 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 65 SER Chi-restraints excluded: chain M residue 309 MET Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 299 CYS 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: 0.7980 chunk 201 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 248 optimal weight: 0.7980 chunk 185 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN ** L 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5456 r_free = 0.5456 target = 0.295212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5182 r_free = 0.5182 target = 0.260851 restraints weight = 48144.444| |-----------------------------------------------------------------------------| r_work (start): 0.5154 rms_B_bonded: 2.88 r_work: 0.5013 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.5013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4557 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 32375 Z= 0.162 Angle : 0.630 18.323 44449 Z= 0.343 Chirality : 0.045 0.424 4901 Planarity : 0.005 0.056 5060 Dihedral : 18.567 179.402 5854 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.16 % Allowed : 12.90 % Favored : 84.94 % 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 are not related in a simple way. whole: -0.85 (0.14), residues: 3386 helix: 1.06 (0.16), residues: 1148 sheet: -0.43 (0.20), residues: 673 loop : -1.91 (0.14), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 481 TYR 0.019 0.001 TYR A 392 PHE 0.039 0.002 PHE M 17 TRP 0.044 0.002 TRP A 20 HIS 0.006 0.001 HIS L 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (32370) covalent geometry : angle 0.63026 / 0.34 (44449) hydrogen bonds : bond 0.04533 / 2.99 ( 1195) hydrogen bonds : angle 5.06095 / 3.53 ( 3388) Misc. bond : bond 0.01170 / 0.59 ( 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 305 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 239 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 GLN cc_start: 0.5638 (OUTLIER) cc_final: 0.5091 (mt0) REVERT: A 211 LYS cc_start: 0.2452 (OUTLIER) cc_final: 0.2104 (mtmt) REVERT: A 277 MET cc_start: -0.1662 (mmm) cc_final: -0.2088 (mmm) REVERT: A 395 MET cc_start: 0.2317 (OUTLIER) cc_final: 0.0007 (tpp) REVERT: B 87 GLU cc_start: 0.5601 (pm20) cc_final: 0.4732 (pm20) REVERT: E 274 GLU cc_start: 0.4088 (OUTLIER) cc_final: 0.3835 (mp0) REVERT: F 14 PHE cc_start: 0.5475 (m-80) cc_final: 0.4361 (m-80) REVERT: F 74 MET cc_start: 0.3813 (tmm) cc_final: 0.3389 (tmm) REVERT: F 223 ILE cc_start: 0.7363 (OUTLIER) cc_final: 0.7034 (mm) REVERT: F 254 TRP cc_start: 0.4347 (m100) cc_final: 0.4052 (m100) REVERT: F 407 ARG cc_start: 0.5653 (ttt180) cc_final: 0.5261 (ttt180) REVERT: I 336 MET cc_start: 0.5216 (mpt) cc_final: 0.4617 (mpt) REVERT: M 126 ARG cc_start: 0.4395 (tpm170) cc_final: 0.4064 (tpm170) REVERT: M 328 LYS cc_start: 0.6842 (ptpt) cc_final: 0.6550 (pmmt) REVERT: N 443 ILE cc_start: 0.0123 (OUTLIER) cc_final: -0.1039 (mt) outliers start: 66 outliers final: 30 residues processed: 285 average time/residue: 0.5188 time to fit residues: 184.6694 Evaluate side-chains 270 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain F residue 221 THR 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 491 THR Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 210 TYR Chi-restraints excluded: chain I residue 327 SER 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 M residue 65 SER Chi-restraints excluded: chain M residue 309 MET Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 256 ILE Chi-restraints excluded: chain N residue 299 CYS Chi-restraints excluded: chain N residue 443 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 207 optimal weight: 4.9990 chunk 232 optimal weight: 0.0870 chunk 222 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 264 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 347 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 244 optimal weight: 1.9990 chunk 302 optimal weight: 0.5980 chunk 146 optimal weight: 9.9990 overall best weight: 1.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS B 66 ASN ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS B 430 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN F 129 ASN ** L 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 ASN N 66 ASN N 129 ASN ** N 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5423 r_free = 0.5423 target = 0.290815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5142 r_free = 0.5142 target = 0.255930 restraints weight = 47281.655| |-----------------------------------------------------------------------------| r_work (start): 0.5108 rms_B_bonded: 2.74 r_work: 0.4955 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4705 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 32375 Z= 0.211 Angle : 0.693 22.058 44449 Z= 0.375 Chirality : 0.047 0.365 4901 Planarity : 0.005 0.058 5060 Dihedral : 18.607 179.055 5854 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.65 % Allowed : 13.52 % Favored : 83.83 % 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 are not related in a simple way. whole: -1.06 (0.14), residues: 3386 helix: 0.81 (0.16), residues: 1145 sheet: -0.37 (0.22), residues: 604 loop : -1.99 (0.14), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 481 TYR 0.023 0.002 TYR N 65 PHE 0.043 0.002 PHE M 17 TRP 0.077 0.003 TRP A 20 HIS 0.011 0.001 HIS L 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 (32370) covalent geometry : angle 0.69255 / 0.37 (44449) hydrogen bonds : bond 0.05167 / 3.44 ( 1195) hydrogen bonds : angle 5.26427 / 3.67 ( 3388) Misc. bond : bond 0.00587 / 0.37 ( 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 331 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 250 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.2686 (OUTLIER) cc_final: 0.2425 (mtmm) REVERT: A 277 MET cc_start: -0.1499 (mmm) cc_final: -0.2142 (mmm) REVERT: A 395 MET cc_start: 0.2347 (OUTLIER) cc_final: 0.0094 (tmt) REVERT: B 6 TYR cc_start: 0.5040 (t80) cc_final: 0.4682 (t80) REVERT: B 25 ASP cc_start: 0.5399 (m-30) cc_final: 0.5151 (t0) REVERT: B 87 GLU cc_start: 0.5921 (pm20) cc_final: 0.5240 (pm20) REVERT: B 341 GLN cc_start: 0.5433 (OUTLIER) cc_final: 0.5107 (pt0) REVERT: E 274 GLU cc_start: 0.4118 (OUTLIER) cc_final: 0.3709 (mp0) REVERT: F 1 MET cc_start: 0.3372 (mmm) cc_final: 0.2966 (mmm) REVERT: F 14 PHE cc_start: 0.5839 (m-80) cc_final: 0.4538 (m-80) REVERT: F 223 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7165 (mm) REVERT: F 407 ARG cc_start: 0.5705 (ttt180) cc_final: 0.5361 (ttt180) REVERT: F 435 MET cc_start: 0.0695 (mtt) cc_final: 0.0419 (mtt) REVERT: I 99 ILE cc_start: 0.6592 (mp) cc_final: 0.6076 (mm) REVERT: I 261 CYS cc_start: 0.6208 (t) cc_final: 0.5984 (p) REVERT: I 336 MET cc_start: 0.5276 (OUTLIER) cc_final: 0.4754 (mpt) REVERT: M 126 ARG cc_start: 0.4539 (tpm170) cc_final: 0.4142 (tpm170) REVERT: N 25 ASP cc_start: 0.6413 (m-30) cc_final: 0.6133 (m-30) REVERT: N 443 ILE cc_start: 0.0436 (OUTLIER) cc_final: -0.0553 (mt) REVERT: N 490 LEU cc_start: 0.5652 (OUTLIER) cc_final: 0.5081 (pt) outliers start: 81 outliers final: 42 residues processed: 308 average time/residue: 0.4881 time to fit residues: 188.3344 Evaluate side-chains 289 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 239 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 21 THR 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 311 THR Chi-restraints excluded: chain B residue 341 GLN Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 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 78 LEU Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 210 TYR Chi-restraints excluded: chain I residue 327 SER Chi-restraints excluded: chain I residue 336 MET Chi-restraints excluded: chain L residue 267 LYS Chi-restraints excluded: chain L residue 281 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 57 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 309 MET Chi-restraints excluded: chain N residue 39 ILE 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 299 CYS Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain N residue 443 ILE Chi-restraints excluded: chain N residue 490 LEU Chi-restraints excluded: chain N residue 507 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 107 optimal weight: 1.9990 chunk 237 optimal weight: 0.4980 chunk 80 optimal weight: 0.7980 chunk 301 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 258 optimal weight: 0.6980 chunk 228 optimal weight: 4.9990 chunk 211 optimal weight: 0.9980 chunk 296 optimal weight: 9.9990 chunk 318 optimal weight: 6.9990 chunk 315 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 GLN ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN ** N 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 HIS ** 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 = 0.5428 r_free = 0.5428 target = 0.291589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5148 r_free = 0.5148 target = 0.256943 restraints weight = 47711.704| |-----------------------------------------------------------------------------| r_work (start): 0.5115 rms_B_bonded: 2.86 r_work: 0.4969 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4676 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32375 Z= 0.160 Angle : 0.634 21.207 44449 Z= 0.343 Chirality : 0.045 0.332 4901 Planarity : 0.005 0.052 5060 Dihedral : 18.544 179.285 5854 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.45 % Allowed : 14.51 % Favored : 83.04 % 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 are not related in a simple way. whole: -0.88 (0.14), residues: 3386 helix: 1.04 (0.16), residues: 1141 sheet: -0.10 (0.22), residues: 593 loop : -2.02 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG M 71 TYR 0.016 0.001 TYR N 65 PHE 0.025 0.002 PHE B 313 TRP 0.055 0.002 TRP A 20 HIS 0.007 0.001 HIS B 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (32370) covalent geometry : angle 0.63351 / 0.34 (44449) hydrogen bonds : bond 0.04464 / 2.97 ( 1195) hydrogen bonds : angle 5.07034 / 3.53 ( 3388) Misc. bond : bond 0.00501 / 0.32 ( 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: 75 poor density : 243 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.2605 (OUTLIER) cc_final: 0.1791 (ttpt) REVERT: A 277 MET cc_start: -0.1314 (mmm) cc_final: -0.2137 (mmm) REVERT: A 395 MET cc_start: 0.2196 (OUTLIER) cc_final: 0.0068 (tmt) REVERT: B 6 TYR cc_start: 0.5114 (t80) cc_final: 0.4766 (t80) REVERT: B 341 GLN cc_start: 0.5369 (OUTLIER) cc_final: 0.5067 (pt0) REVERT: F 1 MET cc_start: 0.3335 (mmm) cc_final: 0.2853 (mmm) REVERT: F 14 PHE cc_start: 0.5706 (m-80) cc_final: 0.4483 (m-80) REVERT: F 223 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.7178 (mm) REVERT: F 407 ARG cc_start: 0.5686 (ttt180) cc_final: 0.5342 (ttt180) REVERT: F 435 MET cc_start: 0.0610 (mtt) cc_final: 0.0316 (mtt) REVERT: I 122 MET cc_start: 0.7037 (OUTLIER) cc_final: 0.6482 (ptp) REVERT: I 336 MET cc_start: 0.5199 (OUTLIER) cc_final: 0.4648 (mpt) REVERT: I 370 ASN cc_start: 0.4591 (OUTLIER) cc_final: 0.4193 (t0) REVERT: M 126 ARG cc_start: 0.4539 (tpm170) cc_final: 0.4143 (tpm170) REVERT: M 336 MET cc_start: 0.4825 (mmm) cc_final: 0.4552 (mpp) REVERT: N 25 ASP cc_start: 0.6364 (m-30) cc_final: 0.6149 (m-30) REVERT: N 443 ILE cc_start: 0.0424 (OUTLIER) cc_final: -0.0599 (mt) REVERT: N 452 ILE cc_start: 0.5925 (OUTLIER) cc_final: 0.5721 (tt) outliers start: 75 outliers final: 43 residues processed: 296 average time/residue: 0.4877 time to fit residues: 182.7961 Evaluate side-chains 286 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 234 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 311 THR 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 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 309 MET Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 364 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 I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 210 TYR Chi-restraints excluded: chain I residue 327 SER Chi-restraints excluded: chain I residue 336 MET Chi-restraints excluded: chain I residue 370 ASN Chi-restraints excluded: chain L residue 219 ILE Chi-restraints excluded: chain L residue 267 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 65 SER Chi-restraints excluded: chain M residue 265 ILE Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 299 CYS Chi-restraints excluded: chain N residue 443 ILE Chi-restraints excluded: chain N residue 452 ILE Chi-restraints excluded: chain N residue 490 LEU Chi-restraints excluded: chain N residue 507 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 50 optimal weight: 7.9990 chunk 175 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 267 optimal weight: 1.9990 chunk 312 optimal weight: 50.0000 chunk 208 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 169 optimal weight: 0.0050 chunk 287 optimal weight: 8.9990 chunk 255 optimal weight: 0.6980 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 HIS I 212 ASN ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 358 HIS ** N 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 454 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5376 r_free = 0.5376 target = 0.284646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5110 r_free = 0.5110 target = 0.251660 restraints weight = 46652.816| |-----------------------------------------------------------------------------| r_work (start): 0.5060 rms_B_bonded: 2.46 r_work: 0.4892 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4876 moved from start: 0.5610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 32375 Z= 0.302 Angle : 0.849 28.967 44449 Z= 0.453 Chirality : 0.053 0.428 4901 Planarity : 0.006 0.098 5060 Dihedral : 18.782 178.497 5854 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 2.91 % Allowed : 15.19 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.14), residues: 3386 helix: 0.21 (0.15), residues: 1137 sheet: -0.53 (0.22), residues: 600 loop : -2.25 (0.14), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 481 TYR 0.032 0.003 TYR N 65 PHE 0.048 0.003 PHE B 365 TRP 0.103 0.004 TRP A 20 HIS 0.014 0.002 HIS L 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.30 (32370) covalent geometry : angle 0.84922 / 0.45 (44449) hydrogen bonds : bond 0.06457 / 4.30 ( 1195) hydrogen bonds : angle 5.79022 / 4.04 ( 3388) Misc. bond : bond 0.00705 / 0.45 ( 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 342 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 253 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.2787 (OUTLIER) cc_final: 0.2281 (mtmp) REVERT: A 277 MET cc_start: -0.1444 (mmm) cc_final: -0.1904 (mmm) REVERT: A 395 MET cc_start: 0.2303 (OUTLIER) cc_final: 0.0078 (tpt) REVERT: B 6 TYR cc_start: 0.5333 (t80) cc_final: 0.4962 (t80) REVERT: F 1 MET cc_start: 0.3498 (mmm) cc_final: 0.2981 (mmm) REVERT: F 14 PHE cc_start: 0.6122 (m-80) cc_final: 0.5036 (m-80) REVERT: F 132 GLU cc_start: 0.2730 (OUTLIER) cc_final: 0.2230 (tp30) REVERT: F 435 MET cc_start: 0.0533 (mtt) cc_final: 0.0241 (mtt) REVERT: I 122 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.6923 (ptp) REVERT: I 336 MET cc_start: 0.5346 (OUTLIER) cc_final: 0.4806 (mpt) REVERT: I 370 ASN cc_start: 0.4820 (OUTLIER) cc_final: 0.4387 (t0) REVERT: L 43 VAL cc_start: 0.5727 (OUTLIER) cc_final: 0.5443 (t) REVERT: L 139 TRP cc_start: 0.6031 (m100) cc_final: 0.4922 (t-100) REVERT: L 419 PHE cc_start: 0.4604 (m-80) cc_final: 0.4204 (m-80) REVERT: M 15 ASN cc_start: 0.1901 (OUTLIER) cc_final: 0.1380 (m-40) REVERT: M 107 ASP cc_start: 0.6893 (m-30) cc_final: 0.6689 (m-30) REVERT: M 126 ARG cc_start: 0.4741 (tpm170) cc_final: 0.4309 (tpm170) REVERT: M 336 MET cc_start: 0.5010 (mmm) cc_final: 0.4595 (mmp) REVERT: N 443 ILE cc_start: 0.0872 (OUTLIER) cc_final: 0.0061 (mt) REVERT: N 490 LEU cc_start: 0.5781 (OUTLIER) cc_final: 0.5355 (pp) outliers start: 89 outliers final: 46 residues processed: 315 average time/residue: 0.5186 time to fit residues: 204.4555 Evaluate side-chains 297 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 241 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 317 VAL 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 99 ILE Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 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 113 VAL Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 336 MET Chi-restraints excluded: chain I residue 370 ASN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 219 ILE Chi-restraints excluded: chain L residue 267 LYS Chi-restraints excluded: chain L residue 281 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 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 M residue 265 ILE Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 256 ILE Chi-restraints excluded: chain N residue 299 CYS Chi-restraints excluded: chain N residue 357 VAL Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain N residue 443 ILE Chi-restraints excluded: chain N residue 490 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 148 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 198 optimal weight: 4.9990 chunk 265 optimal weight: 0.5980 chunk 211 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 chunk 274 optimal weight: 0.0970 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN F 207 HIS I 254 ASN ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN M 358 HIS ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5398 r_free = 0.5398 target = 0.287801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5121 r_free = 0.5121 target = 0.252992 restraints weight = 46778.013| |-----------------------------------------------------------------------------| r_work (start): 0.5086 rms_B_bonded: 2.69 r_work: 0.4931 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4794 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32375 Z= 0.167 Angle : 0.684 25.302 44449 Z= 0.367 Chirality : 0.046 0.351 4901 Planarity : 0.005 0.057 5060 Dihedral : 18.622 178.848 5854 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.93 % Allowed : 16.60 % Favored : 81.48 % 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 are not related in a simple way. whole: -1.29 (0.14), residues: 3386 helix: 0.64 (0.16), residues: 1136 sheet: -0.43 (0.22), residues: 604 loop : -2.17 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 72 TYR 0.017 0.001 TYR N 65 PHE 0.033 0.002 PHE I 120 TRP 0.101 0.003 TRP A 20 HIS 0.006 0.001 HIS B 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (32370) covalent geometry : angle 0.68362 / 0.37 (44449) hydrogen bonds : bond 0.04816 / 3.22 ( 1195) hydrogen bonds : angle 5.30586 / 3.71 ( 3388) Misc. bond : bond 0.00540 / 0.34 ( 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 296 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 237 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.2661 (OUTLIER) cc_final: 0.2149 (mtmt) REVERT: A 277 MET cc_start: -0.1668 (mmm) cc_final: -0.2075 (mmm) REVERT: A 328 LYS cc_start: 0.6473 (OUTLIER) cc_final: 0.6205 (tttt) REVERT: A 392 TYR cc_start: 0.6339 (OUTLIER) cc_final: 0.5850 (p90) REVERT: A 395 MET cc_start: 0.2215 (OUTLIER) cc_final: 0.0016 (tpt) REVERT: B 6 TYR cc_start: 0.5194 (t80) cc_final: 0.4869 (t80) REVERT: F 1 MET cc_start: 0.3535 (mmm) cc_final: 0.2816 (mmm) REVERT: F 14 PHE cc_start: 0.5849 (m-80) cc_final: 0.4613 (m-80) REVERT: F 132 GLU cc_start: 0.2733 (OUTLIER) cc_final: 0.2297 (tp30) REVERT: I 122 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6712 (ptp) REVERT: I 336 MET cc_start: 0.5220 (OUTLIER) cc_final: 0.4662 (mpt) REVERT: I 370 ASN cc_start: 0.4732 (OUTLIER) cc_final: 0.4330 (t0) REVERT: L 43 VAL cc_start: 0.5675 (OUTLIER) cc_final: 0.5417 (t) REVERT: L 139 TRP cc_start: 0.5971 (m100) cc_final: 0.5592 (t-100) REVERT: L 419 PHE cc_start: 0.4257 (m-80) cc_final: 0.3894 (m-80) REVERT: M 336 MET cc_start: 0.4722 (mmm) cc_final: 0.4515 (mmt) REVERT: N 19 LYS cc_start: 0.7654 (mtpp) cc_final: 0.6704 (mptp) REVERT: N 443 ILE cc_start: 0.0794 (OUTLIER) cc_final: -0.0170 (mt) outliers start: 59 outliers final: 35 residues processed: 280 average time/residue: 0.5041 time to fit residues: 175.7226 Evaluate side-chains 277 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 232 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 5 ILE 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 412 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 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 113 VAL Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 336 MET Chi-restraints excluded: chain I residue 370 ASN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 219 ILE Chi-restraints excluded: chain L residue 267 LYS Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain M residue 265 ILE Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain N residue 299 CYS Chi-restraints excluded: chain N residue 443 ILE Chi-restraints excluded: chain N residue 490 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 100 optimal weight: 0.9990 chunk 286 optimal weight: 2.9990 chunk 259 optimal weight: 0.2980 chunk 91 optimal weight: 0.5980 chunk 273 optimal weight: 1.9990 chunk 341 optimal weight: 5.9990 chunk 291 optimal weight: 10.0000 chunk 306 optimal weight: 0.8980 chunk 311 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN F 207 HIS F 325 ASN I 69 ASN L 251 HIS ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 358 HIS N 217 HIS ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 446 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5390 r_free = 0.5390 target = 0.286685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5127 r_free = 0.5127 target = 0.253724 restraints weight = 46839.728| |-----------------------------------------------------------------------------| r_work (start): 0.5087 rms_B_bonded: 2.62 r_work: 0.4923 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4813 moved from start: 0.5925 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= 0.191 Angle : 0.707 25.297 44449 Z= 0.376 Chirality : 0.047 0.378 4901 Planarity : 0.005 0.056 5060 Dihedral : 18.569 178.543 5854 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.80 % Allowed : 16.82 % Favored : 81.38 % 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 are not related in a simple way. whole: -1.32 (0.14), residues: 3386 helix: 0.62 (0.16), residues: 1135 sheet: -0.46 (0.22), residues: 600 loop : -2.19 (0.14), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 481 TYR 0.035 0.002 TYR E 171 PHE 0.032 0.002 PHE I 120 TRP 0.119 0.003 TRP A 20 HIS 0.006 0.001 HIS L 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (32370) covalent geometry : angle 0.70720 / 0.38 (44449) hydrogen bonds : bond 0.05016 / 3.33 ( 1195) hydrogen bonds : angle 5.33053 / 3.73 ( 3388) Misc. bond : bond 0.00569 / 0.36 ( 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 290 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 235 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.2787 (OUTLIER) cc_final: 0.1929 (ttmt) REVERT: A 277 MET cc_start: -0.1353 (mmm) cc_final: -0.2375 (mmm) REVERT: A 395 MET cc_start: 0.2126 (OUTLIER) cc_final: -0.0027 (tmt) REVERT: B 6 TYR cc_start: 0.5215 (t80) cc_final: 0.4864 (t80) REVERT: B 341 GLN cc_start: 0.5378 (OUTLIER) cc_final: 0.5091 (pt0) REVERT: F 1 MET cc_start: 0.3929 (mmm) cc_final: 0.3297 (mmm) REVERT: F 14 PHE cc_start: 0.5942 (m-80) cc_final: 0.4631 (m-80) REVERT: F 132 GLU cc_start: 0.2961 (OUTLIER) cc_final: 0.2574 (tp30) REVERT: I 122 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.6684 (ptp) REVERT: I 336 MET cc_start: 0.5306 (mpt) cc_final: 0.4749 (mpt) REVERT: I 370 ASN cc_start: 0.4736 (OUTLIER) cc_final: 0.4310 (t0) REVERT: L 43 VAL cc_start: 0.5733 (OUTLIER) cc_final: 0.5446 (t) REVERT: L 139 TRP cc_start: 0.5981 (m100) cc_final: 0.5612 (t-100) REVERT: L 419 PHE cc_start: 0.4244 (m-80) cc_final: 0.3898 (m-80) REVERT: M 15 ASN cc_start: 0.1857 (OUTLIER) cc_final: 0.1308 (m-40) REVERT: N 19 LYS cc_start: 0.7639 (mtpp) cc_final: 0.6719 (mptp) REVERT: N 443 ILE cc_start: 0.0924 (OUTLIER) cc_final: -0.0043 (mt) outliers start: 55 outliers final: 38 residues processed: 279 average time/residue: 0.4668 time to fit residues: 161.8730 Evaluate side-chains 276 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 229 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 341 GLN Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain 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 309 MET Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 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 113 VAL Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 370 ASN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 219 ILE Chi-restraints excluded: chain L residue 267 LYS Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain M residue 15 ASN Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain N residue 256 ILE Chi-restraints excluded: chain N residue 299 CYS Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain N residue 443 ILE Chi-restraints excluded: chain N residue 490 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 205 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 218 optimal weight: 1.9990 chunk 124 optimal weight: 0.0270 chunk 185 optimal weight: 0.9990 chunk 320 optimal weight: 0.0030 chunk 331 optimal weight: 0.6980 chunk 223 optimal weight: 5.9990 chunk 281 optimal weight: 7.9990 chunk 110 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 overall best weight: 0.4850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 HIS ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 358 HIS ** N 341 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 = 0.5405 r_free = 0.5405 target = 0.288770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5125 r_free = 0.5125 target = 0.253841 restraints weight = 47206.967| |-----------------------------------------------------------------------------| r_work (start): 0.5092 rms_B_bonded: 2.86 r_work: 0.4936 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4776 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32375 Z= 0.145 Angle : 0.662 22.262 44449 Z= 0.350 Chirality : 0.046 0.602 4901 Planarity : 0.005 0.052 5060 Dihedral : 18.483 179.103 5854 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.40 % Allowed : 17.38 % Favored : 81.22 % 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 are not related in a simple way. whole: -1.17 (0.14), residues: 3386 helix: 0.77 (0.16), residues: 1147 sheet: -0.50 (0.21), residues: 640 loop : -2.12 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 263 TYR 0.017 0.001 TYR F 65 PHE 0.029 0.002 PHE B 313 TRP 0.110 0.002 TRP A 20 HIS 0.004 0.001 HIS B 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (32370) covalent geometry : angle 0.66186 / 0.35 (44449) hydrogen bonds : bond 0.04327 / 2.89 ( 1195) hydrogen bonds : angle 5.07148 / 3.54 ( 3388) Misc. bond : bond 0.00459 / 0.28 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11624.01 seconds wall clock time: 198 minutes 37.57 seconds (11917.57 seconds total)