Starting phenix.real_space_refine on Mon Jul 6 00:32:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8spo_40680/07_2026/8spo_40680_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8spo_40680/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8spo_40680/07_2026/8spo_40680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8spo_40680/07_2026/8spo_40680.map" model { file = "/net/cci-nas-00/data/ceres_data/8spo_40680/07_2026/8spo_40680_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8spo_40680/07_2026/8spo_40680_neut.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 158 5.49 5 Mg 4 5.21 5 S 85 5.16 5 C 19663 2.51 5 N 5212 2.21 5 O 6185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 6.86, per 1000 atoms: 0.22 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: 2.82 Conformation dependent library (CDL) restraints added in 1.3 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: 3.18 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: 6.34 Time building geometry restraints manager: 3.72 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: 43439 1.81 - 3.61: 892 3.61 - 5.42: 102 5.42 - 7.22: 11 7.22 - 9.03: 5 Bond angle restraints: 44449 Sorted by residual: angle pdb=" N ASN E 48 " pdb=" CA ASN E 48 " pdb=" C ASN E 48 " ideal model delta sigma weight residual 113.72 104.86 8.86 1.30e+00 5.92e-01 4.64e+01 angle pdb=" C ASN E 48 " pdb=" CA ASN E 48 " pdb=" CB ASN E 48 " ideal model delta sigma weight residual 109.55 118.58 -9.03 1.68e+00 3.54e-01 2.89e+01 angle pdb=" N SER A 148 " pdb=" CA SER A 148 " pdb=" C SER A 148 " ideal model delta sigma weight residual 111.28 105.58 5.70 1.09e+00 8.42e-01 2.74e+01 angle pdb=" CA ILE E 157 " pdb=" C ILE E 157 " pdb=" O ILE E 157 " ideal model delta sigma weight residual 121.98 115.83 6.15 1.21e+00 6.83e-01 2.59e+01 angle pdb=" C VAL M 164 " pdb=" N ILE M 165 " pdb=" CA ILE M 165 " ideal model delta sigma weight residual 123.19 117.09 6.10 1.24e+00 6.50e-01 2.42e+01 ... (remaining 44444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 18641 35.93 - 71.85: 616 71.85 - 107.78: 44 107.78 - 143.70: 9 143.70 - 179.63: 32 Dihedral angle restraints: 19342 sinusoidal: 9256 harmonic: 10086 Sorted by residual: dihedral pdb=" O4' U J 17 " pdb=" C1' U J 17 " pdb=" N1 U J 17 " pdb=" C2 U J 17 " ideal model delta sinusoidal sigma weight residual -160.00 19.63 -179.63 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U O 17 " pdb=" C1' U O 17 " pdb=" N1 U O 17 " pdb=" C2 U O 17 " ideal model delta sinusoidal sigma weight residual -160.00 19.61 -179.61 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U G 13 " pdb=" C1' U G 13 " pdb=" N1 U G 13 " pdb=" C2 U G 13 " ideal model delta sinusoidal sigma weight residual -160.00 16.40 -176.40 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 19339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.105: 4889 1.105 - 2.210: 0 2.210 - 3.315: 0 3.315 - 4.421: 0 4.421 - 5.526: 12 Chirality restraints: 4901 Sorted by residual: chirality pdb=" C3D NAD E 501 " pdb=" C2D NAD E 501 " pdb=" C4D NAD E 501 " pdb=" O3D NAD E 501 " both_signs ideal model delta sigma weight residual False -2.73 2.80 -5.53 2.00e-01 2.50e+01 7.63e+02 chirality pdb=" C3D NAD I 501 " pdb=" C2D NAD I 501 " pdb=" C4D NAD I 501 " pdb=" O3D NAD I 501 " both_signs ideal model delta sigma weight residual False -2.73 2.79 -5.51 2.00e-01 2.50e+01 7.60e+02 chirality pdb=" C3B NAD E 501 " pdb=" C2B NAD E 501 " pdb=" C4B NAD E 501 " pdb=" O3B NAD E 501 " both_signs ideal model delta sigma weight residual False -2.71 2.71 -5.42 2.00e-01 2.50e+01 7.35e+02 ... (remaining 4898 not shown) Planarity restraints: 5060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 146 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C ASP A 146 " -0.063 2.00e-02 2.50e+03 pdb=" O ASP A 146 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA A 147 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR M 154 " -0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C TYR M 154 " 0.057 2.00e-02 2.50e+03 pdb=" O TYR M 154 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN M 155 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 105 " -0.033 2.00e-02 2.50e+03 1.97e-02 7.78e+00 pdb=" CG TYR A 105 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 105 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 105 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 105 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 105 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 105 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 105 " -0.009 2.00e-02 2.50e+03 ... (remaining 5057 not shown) Histogram of nonbonded interaction distances: 0.33 - 1.25: 32 1.25 - 2.16: 190 2.16 - 3.07: 20655 3.07 - 3.99: 79333 3.99 - 4.90: 151707 Warning: very small nonbonded interaction distances. Nonbonded interactions: 251917 Sorted by model distance: nonbonded pdb=" CD LYS B 504 " pdb=" CA ASP F 133 " model vdw 0.334 3.870 nonbonded pdb=" NZ LYS B 504 " pdb=" N GLU F 134 " model vdw 0.498 3.200 nonbonded pdb=" C ASP L 133 " pdb=" CE LYS N 504 " model vdw 0.589 3.670 nonbonded pdb=" CB LYS B 504 " pdb=" OD1 ASP F 133 " model vdw 0.663 3.440 nonbonded pdb=" CG ASP L 137 " pdb=" OD1 ASN N 135 " model vdw 0.666 3.270 ... (remaining 251912 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 156 or resid 169 through 186 or resid 200 throug \ h 216 or resid 241 through 420)) selection = (chain 'E' and (resid 2 through 156 or resid 169 through 238 or resid 241 throug \ h 296 or resid 309 through 420)) selection = (chain 'I' and (resid 2 through 216 or resid 241 through 296 or resid 309 throug \ h 420)) selection = (chain 'M' and (resid 2 through 156 or resid 169 through 186 or resid 200 throug \ h 216 or resid 241 through 296 or resid 309 through 420)) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 1 through 19) selection = (chain 'J' and resid 1 through 19) selection = chain 'O' } ncs_group { reference = (chain 'D' and resid 8 through 23) selection = (chain 'H' and resid 8 through 23) selection = (chain 'K' and resid 8 through 23) selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.500 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.730 ------------------------------------------------------------------------------- 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= 0.598 Angle : 0.617 9.028 44449 Z= 0.411 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 0.00383 / 0.26 (32370) covalent geometry : angle 0.61715 / 0.41 (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 : 1.001 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: 0.5302 time to fit residues: 198.6081 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 : 0.818 ------------------------------------------------------------------------------- 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 217 HIS ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 446 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5534 r_free = 0.5534 target = 0.306795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5298 r_free = 0.5298 target = 0.276527 restraints weight = 50388.925| |-----------------------------------------------------------------------------| r_work (start): 0.5284 rms_B_bonded: 2.76 r_work: 0.5174 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.5174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4102 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.152 32375 Z= 0.216 Angle : 0.745 15.520 44449 Z= 0.399 Chirality : 0.051 0.675 4901 Planarity : 0.005 0.075 5060 Dihedral : 19.152 179.732 5856 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.31 % Allowed : 6.17 % Favored : 92.52 % 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: -1.03 (0.14), residues: 3386 helix: 0.96 (0.16), residues: 1140 sheet: -0.74 (0.19), residues: 683 loop : -1.94 (0.14), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 114 TYR 0.026 0.002 TYR M 210 PHE 0.044 0.003 PHE B 503 TRP 0.019 0.002 TRP N 370 HIS 0.011 0.001 HIS I 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.22 (32370) covalent geometry : angle 0.74522 / 0.40 (44449) hydrogen bonds : bond 0.05599 / 3.62 ( 1195) hydrogen bonds : angle 5.45442 / 3.82 ( 3388) Misc. bond : bond 0.01434 / 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 295 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 255 time to evaluate : 0.947 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: -0.1377 (mmm) cc_final: -0.2209 (mmm) REVERT: A 395 MET cc_start: 0.2517 (OUTLIER) cc_final: -0.0284 (tpp) REVERT: B 39 ILE cc_start: 0.4281 (mt) cc_final: 0.4078 (mm) REVERT: B 336 LYS cc_start: 0.3619 (mttp) cc_final: 0.3399 (mttt) REVERT: B 345 SER cc_start: 0.5896 (t) cc_final: 0.5390 (m) REVERT: E 274 GLU cc_start: 0.4260 (OUTLIER) cc_final: 0.3530 (mp0) REVERT: F 79 GLU cc_start: 0.4693 (tp30) cc_final: 0.3614 (mm-30) REVERT: F 254 TRP cc_start: 0.3947 (m100) cc_final: 0.3715 (m100) REVERT: I 35 ASP cc_start: 0.5790 (OUTLIER) cc_final: 0.5251 (t70) REVERT: I 336 MET cc_start: 0.4699 (mpt) cc_final: 0.4303 (mpt) REVERT: M 17 PHE cc_start: 0.2408 (t80) cc_final: 0.1980 (t80) REVERT: M 374 ARG cc_start: 0.3345 (tmm-80) cc_final: 0.3140 (tmm-80) REVERT: N 19 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6495 (mptp) REVERT: N 281 LEU cc_start: 0.6613 (tp) cc_final: 0.6409 (mp) outliers start: 40 outliers final: 15 residues processed: 271 average time/residue: 0.5312 time to fit residues: 175.5457 Evaluate side-chains 258 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 239 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 74 MET 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 122 ILE Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 19 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 95 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 288 optimal weight: 3.9990 chunk 291 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 218 optimal weight: 0.8980 chunk 328 optimal weight: 0.6980 chunk 113 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 ASN A 156 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** 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 251 HIS 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5474 r_free = 0.5474 target = 0.298420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5215 r_free = 0.5215 target = 0.265309 restraints weight = 48885.717| |-----------------------------------------------------------------------------| r_work (start): 0.5185 rms_B_bonded: 2.89 r_work: 0.5030 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.5030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4469 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 32375 Z= 0.213 Angle : 0.703 16.578 44449 Z= 0.382 Chirality : 0.048 0.319 4901 Planarity : 0.005 0.060 5060 Dihedral : 18.772 179.362 5854 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.19 % Allowed : 9.21 % Favored : 88.60 % 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: -1.02 (0.14), residues: 3386 helix: 0.91 (0.16), residues: 1151 sheet: -0.60 (0.20), residues: 660 loop : -1.96 (0.14), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 481 TYR 0.031 0.002 TYR N 505 PHE 0.029 0.003 PHE F 78 TRP 0.026 0.002 TRP M 175 HIS 0.010 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.21 (32370) covalent geometry : angle 0.70269 / 0.38 (44449) hydrogen bonds : bond 0.05266 / 3.47 ( 1195) hydrogen bonds : angle 5.24752 / 3.65 ( 3388) Misc. bond : bond 0.00950 / 0.51 ( 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 320 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 253 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 GLN cc_start: 0.5626 (OUTLIER) cc_final: 0.5059 (mt0) REVERT: A 211 LYS cc_start: 0.2198 (OUTLIER) cc_final: 0.1841 (mtmt) REVERT: A 277 MET cc_start: -0.1790 (mmm) cc_final: -0.2306 (mmm) REVERT: A 395 MET cc_start: 0.2460 (OUTLIER) cc_final: -0.0074 (tpp) REVERT: B 21 THR cc_start: 0.7107 (t) cc_final: 0.6531 (m) REVERT: B 141 VAL cc_start: 0.7769 (t) cc_final: 0.7558 (m) REVERT: B 345 SER cc_start: 0.5741 (t) cc_final: 0.5220 (m) REVERT: E 271 LYS cc_start: 0.5913 (mmmt) cc_final: 0.5639 (mmmt) REVERT: E 274 GLU cc_start: 0.4118 (OUTLIER) cc_final: 0.3448 (mp0) REVERT: F 1 MET cc_start: 0.3605 (mmm) cc_final: 0.3251 (mmm) REVERT: F 14 PHE cc_start: 0.5359 (m-80) cc_final: 0.4784 (m-80) REVERT: F 407 ARG cc_start: 0.5697 (ttt180) cc_final: 0.5203 (ttt180) REVERT: I 35 ASP cc_start: 0.6604 (OUTLIER) cc_final: 0.5851 (t70) REVERT: I 323 ILE cc_start: 0.6392 (OUTLIER) cc_final: 0.5826 (mt) REVERT: I 336 MET cc_start: 0.5014 (mpt) cc_final: 0.4547 (mpt) outliers start: 67 outliers final: 21 residues processed: 297 average time/residue: 0.5010 time to fit residues: 184.9001 Evaluate side-chains 266 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 239 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 257 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 344 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain 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 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 N residue 41 SER Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 256 ILE Chi-restraints excluded: chain N residue 299 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 301 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 289 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 44 optimal weight: 2.9990 chunk 192 optimal weight: 0.0040 chunk 88 optimal weight: 2.9990 chunk 278 optimal weight: 0.0670 chunk 6 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.3732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 HIS E 15 ASN F 414 ASN L 349 GLN L 360 HIS ** N 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5490 r_free = 0.5490 target = 0.299846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5229 r_free = 0.5229 target = 0.266925 restraints weight = 48809.737| |-----------------------------------------------------------------------------| r_work (start): 0.5205 rms_B_bonded: 2.89 r_work: 0.5079 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.5079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4377 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32375 Z= 0.132 Angle : 0.583 14.244 44449 Z= 0.321 Chirality : 0.044 0.277 4901 Planarity : 0.004 0.054 5060 Dihedral : 18.617 179.731 5854 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.89 % Allowed : 10.45 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.14), residues: 3386 helix: 1.24 (0.16), residues: 1146 sheet: -0.48 (0.20), residues: 693 loop : -1.92 (0.14), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 481 TYR 0.016 0.001 TYR N 397 PHE 0.030 0.002 PHE I 17 TRP 0.016 0.001 TRP N 370 HIS 0.004 0.001 HIS L 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (32370) covalent geometry : angle 0.58265 / 0.32 (44449) hydrogen bonds : bond 0.04194 / 2.75 ( 1195) hydrogen bonds : angle 4.94783 / 3.45 ( 3388) Misc. bond : bond 0.00408 / 0.25 ( 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 300 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 242 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.1969 (OUTLIER) cc_final: 0.1704 (mtmt) REVERT: A 277 MET cc_start: -0.1713 (mmm) cc_final: -0.2374 (mmm) REVERT: A 279 ASP cc_start: 0.0061 (t0) cc_final: -0.0518 (t0) REVERT: A 395 MET cc_start: 0.2301 (OUTLIER) cc_final: 0.0006 (tpp) REVERT: B 141 VAL cc_start: 0.7745 (t) cc_final: 0.7538 (m) REVERT: B 456 LEU cc_start: 0.1167 (OUTLIER) cc_final: 0.0246 (mp) REVERT: E 274 GLU cc_start: 0.4149 (OUTLIER) cc_final: 0.3641 (mp0) REVERT: F 1 MET cc_start: 0.3588 (mmm) cc_final: 0.3199 (mmm) REVERT: F 14 PHE cc_start: 0.5215 (m-80) cc_final: 0.4593 (m-80) REVERT: F 364 ARG cc_start: 0.5342 (OUTLIER) cc_final: 0.3910 (mmm-85) REVERT: F 407 ARG cc_start: 0.5567 (ttt180) cc_final: 0.5145 (ttt180) REVERT: I 323 ILE cc_start: 0.6261 (OUTLIER) cc_final: 0.5707 (mt) REVERT: I 336 MET cc_start: 0.4995 (OUTLIER) cc_final: 0.4480 (mpt) REVERT: N 19 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6477 (mmtp) REVERT: N 443 ILE cc_start: -0.0123 (OUTLIER) cc_final: -0.0459 (tt) outliers start: 58 outliers final: 24 residues processed: 279 average time/residue: 0.5783 time to fit residues: 198.3421 Evaluate side-chains 264 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 456 LEU 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 19 LYS Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 364 ARG 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 65 SER Chi-restraints excluded: chain M residue 161 ASP Chi-restraints excluded: chain M residue 309 MET Chi-restraints excluded: chain M residue 372 THR Chi-restraints excluded: chain N residue 19 LYS Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 299 CYS Chi-restraints excluded: chain N residue 377 THR 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: 2.9990 chunk 201 optimal weight: 5.9990 chunk 251 optimal weight: 3.9990 chunk 248 optimal weight: 0.0570 chunk 185 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 85 optimal weight: 0.2980 chunk 12 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 341 GLN F 66 ASN N 205 GLN N 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5472 r_free = 0.5472 target = 0.297542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5193 r_free = 0.5193 target = 0.263274 restraints weight = 48589.282| |-----------------------------------------------------------------------------| r_work (start): 0.5169 rms_B_bonded: 3.11 r_work: 0.5037 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.5037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4481 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 32375 Z= 0.144 Angle : 0.597 14.692 44449 Z= 0.326 Chirality : 0.045 0.334 4901 Planarity : 0.004 0.050 5060 Dihedral : 18.546 179.743 5854 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.42 % Allowed : 11.53 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z 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: -0.72 (0.14), residues: 3386 helix: 1.19 (0.16), residues: 1152 sheet: -0.31 (0.20), residues: 649 loop : -1.88 (0.14), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 481 TYR 0.023 0.001 TYR B 6 PHE 0.041 0.002 PHE M 17 TRP 0.058 0.002 TRP E 20 HIS 0.006 0.001 HIS L 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (32370) covalent geometry : angle 0.59684 / 0.33 (44449) hydrogen bonds : bond 0.04229 / 2.79 ( 1195) hydrogen bonds : angle 4.89600 / 3.41 ( 3388) Misc. bond : bond 0.00352 / 0.23 ( 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 319 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 245 time to evaluate : 1.103 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 211 LYS cc_start: 0.2254 (OUTLIER) cc_final: 0.1577 (ttpt) REVERT: A 277 MET cc_start: -0.1654 (mmm) cc_final: -0.2097 (mmm) REVERT: A 395 MET cc_start: 0.2276 (OUTLIER) cc_final: -0.0011 (tpp) REVERT: B 6 TYR cc_start: 0.4583 (t80) cc_final: 0.4269 (t80) REVERT: B 129 ASN cc_start: 0.2479 (OUTLIER) cc_final: 0.2274 (p0) REVERT: B 456 LEU cc_start: 0.1261 (OUTLIER) cc_final: 0.0382 (mp) REVERT: E 274 GLU cc_start: 0.4196 (OUTLIER) cc_final: 0.3909 (mp0) REVERT: F 1 MET cc_start: 0.3596 (mmm) cc_final: 0.3162 (mmm) REVERT: F 14 PHE cc_start: 0.5574 (m-80) cc_final: 0.4546 (m-80) REVERT: F 74 MET cc_start: 0.3755 (tmm) cc_final: 0.3325 (tmm) REVERT: F 223 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.7028 (mm) REVERT: F 254 TRP cc_start: 0.4243 (m100) cc_final: 0.3950 (m100) REVERT: F 364 ARG cc_start: 0.5390 (OUTLIER) cc_final: 0.3925 (mmm-85) REVERT: F 407 ARG cc_start: 0.5627 (ttt180) cc_final: 0.5184 (ttt180) REVERT: I 336 MET cc_start: 0.5123 (OUTLIER) cc_final: 0.4580 (mpt) REVERT: N 19 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6731 (mptp) outliers start: 74 outliers final: 32 residues processed: 294 average time/residue: 0.5019 time to fit residues: 184.2331 Evaluate side-chains 277 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 236 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 59 LYS 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 74 MET Chi-restraints excluded: chain B residue 89 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 456 LEU 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 F residue 44 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 364 ARG 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 43 VAL Chi-restraints excluded: chain I residue 78 LEU 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 479 THR Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 19 LYS Chi-restraints excluded: chain N residue 41 SER 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 Chi-restraints excluded: chain N residue 490 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 207 optimal weight: 7.9990 chunk 232 optimal weight: 0.7980 chunk 222 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 264 optimal weight: 0.9990 chunk 251 optimal weight: 1.9990 chunk 347 optimal weight: 0.0270 chunk 28 optimal weight: 9.9990 chunk 244 optimal weight: 0.6980 chunk 302 optimal weight: 0.8980 chunk 146 optimal weight: 20.0000 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 ASN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 ASN N 205 GLN ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5461 r_free = 0.5461 target = 0.296036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5180 r_free = 0.5180 target = 0.262147 restraints weight = 48027.865| |-----------------------------------------------------------------------------| r_work (start): 0.5156 rms_B_bonded: 3.05 r_work: 0.5016 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.5016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4532 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 32375 Z= 0.153 Angle : 0.595 15.937 44449 Z= 0.327 Chirality : 0.044 0.304 4901 Planarity : 0.004 0.051 5060 Dihedral : 18.518 179.940 5854 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.06 % Allowed : 12.90 % Favored : 85.04 % 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: -0.71 (0.14), residues: 3386 helix: 1.22 (0.16), residues: 1154 sheet: -0.28 (0.20), residues: 647 loop : -1.90 (0.14), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 481 TYR 0.017 0.001 TYR B 6 PHE 0.040 0.002 PHE M 17 TRP 0.035 0.002 TRP M 369 HIS 0.006 0.001 HIS B 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (32370) covalent geometry : angle 0.59512 / 0.33 (44449) hydrogen bonds : bond 0.04248 / 2.81 ( 1195) hydrogen bonds : angle 4.87006 / 3.41 ( 3388) Misc. bond : bond 0.00708 / 0.38 ( 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 306 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 243 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.2343 (OUTLIER) cc_final: 0.1638 (ttpt) REVERT: A 277 MET cc_start: -0.1753 (mmm) cc_final: -0.2179 (mmm) REVERT: A 395 MET cc_start: 0.2236 (OUTLIER) cc_final: 0.0008 (tpp) REVERT: B 456 LEU cc_start: 0.1097 (OUTLIER) cc_final: 0.0399 (mp) REVERT: F 1 MET cc_start: 0.3584 (mmm) cc_final: 0.3174 (mmm) REVERT: F 14 PHE cc_start: 0.5501 (m-80) cc_final: 0.4438 (m-80) REVERT: F 74 MET cc_start: 0.3758 (tmm) cc_final: 0.3438 (tmm) REVERT: F 223 ILE cc_start: 0.7382 (OUTLIER) cc_final: 0.7068 (mm) REVERT: F 254 TRP cc_start: 0.4312 (m100) cc_final: 0.4034 (m100) REVERT: F 364 ARG cc_start: 0.5470 (OUTLIER) cc_final: 0.3860 (mmm160) REVERT: F 407 ARG cc_start: 0.5636 (ttt180) cc_final: 0.5196 (ttt180) REVERT: I 99 ILE cc_start: 0.5971 (mm) cc_final: 0.5767 (mm) REVERT: I 323 ILE cc_start: 0.6734 (OUTLIER) cc_final: 0.6354 (mt) REVERT: I 336 MET cc_start: 0.5194 (OUTLIER) cc_final: 0.4705 (mpt) REVERT: M 128 LEU cc_start: 0.3911 (tt) cc_final: 0.3681 (tt) REVERT: N 19 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6681 (mmtp) outliers start: 63 outliers final: 32 residues processed: 279 average time/residue: 0.4842 time to fit residues: 168.5408 Evaluate side-chains 277 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 237 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 59 LYS 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 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 456 LEU 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 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 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 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 33 TRP Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 19 LYS Chi-restraints excluded: chain N residue 41 SER 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 377 THR Chi-restraints excluded: chain N residue 429 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 107 optimal weight: 0.6980 chunk 237 optimal weight: 0.5980 chunk 80 optimal weight: 0.0970 chunk 301 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 258 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 211 optimal weight: 0.8980 chunk 296 optimal weight: 2.9990 chunk 318 optimal weight: 5.9990 chunk 315 optimal weight: 0.0870 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 GLN F 34 ASN ** L 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5462 r_free = 0.5462 target = 0.296247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5185 r_free = 0.5185 target = 0.262247 restraints weight = 48307.226| |-----------------------------------------------------------------------------| r_work (start): 0.5158 rms_B_bonded: 2.95 r_work: 0.5023 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.5023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4517 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 32375 Z= 0.133 Angle : 0.583 15.410 44449 Z= 0.318 Chirality : 0.044 0.284 4901 Planarity : 0.004 0.052 5060 Dihedral : 18.468 179.963 5854 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.16 % Allowed : 13.36 % Favored : 84.48 % 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: -0.64 (0.14), residues: 3386 helix: 1.33 (0.16), residues: 1155 sheet: -0.37 (0.20), residues: 690 loop : -1.88 (0.14), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 481 TYR 0.028 0.001 TYR B 6 PHE 0.036 0.002 PHE I 17 TRP 0.068 0.002 TRP E 20 HIS 0.007 0.001 HIS M 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (32370) covalent geometry : angle 0.58315 / 0.32 (44449) hydrogen bonds : bond 0.03928 / 2.58 ( 1195) hydrogen bonds : angle 4.73336 / 3.31 ( 3388) Misc. bond : bond 0.00406 / 0.26 ( 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 307 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 241 time to evaluate : 1.152 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 211 LYS cc_start: 0.2366 (OUTLIER) cc_final: 0.2007 (mtmm) REVERT: A 277 MET cc_start: -0.1442 (mmm) cc_final: -0.2355 (mmm) REVERT: A 395 MET cc_start: 0.2124 (OUTLIER) cc_final: 0.0155 (tmt) REVERT: B 6 TYR cc_start: 0.4777 (t80) cc_final: 0.4388 (t80) REVERT: B 249 GLU cc_start: 0.5088 (tp30) cc_final: 0.4876 (tp30) REVERT: B 456 LEU cc_start: 0.1202 (OUTLIER) cc_final: 0.0538 (mt) REVERT: F 1 MET cc_start: 0.3579 (mmm) cc_final: 0.3154 (mmm) REVERT: F 14 PHE cc_start: 0.5476 (m-80) cc_final: 0.4378 (m-80) REVERT: F 223 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.7090 (mm) REVERT: F 364 ARG cc_start: 0.5468 (OUTLIER) cc_final: 0.3790 (mmm160) REVERT: F 407 ARG cc_start: 0.5600 (ttt180) cc_final: 0.5196 (ttt180) REVERT: F 435 MET cc_start: 0.0713 (mtt) cc_final: 0.0389 (mtt) REVERT: I 122 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6493 (ptp) REVERT: I 336 MET cc_start: 0.5188 (OUTLIER) cc_final: 0.4641 (mpt) REVERT: M 168 GLU cc_start: 0.4249 (tp30) cc_final: 0.3879 (tp30) REVERT: N 19 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6654 (mmtp) REVERT: N 256 ILE cc_start: 0.5101 (OUTLIER) cc_final: 0.4719 (tt) outliers start: 66 outliers final: 32 residues processed: 280 average time/residue: 0.4930 time to fit residues: 172.9997 Evaluate side-chains 276 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 235 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS 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 311 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 456 LEU 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 F residue 29 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 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 65 SER Chi-restraints excluded: chain I residue 78 LEU 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 L residue 267 LYS Chi-restraints excluded: chain L residue 384 VAL 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 N residue 19 LYS 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 377 THR Chi-restraints excluded: chain N residue 490 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 50 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 148 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 chunk 267 optimal weight: 3.9990 chunk 312 optimal weight: 40.0000 chunk 208 optimal weight: 7.9990 chunk 157 optimal weight: 0.0060 chunk 169 optimal weight: 0.0170 chunk 287 optimal weight: 8.9990 chunk 255 optimal weight: 1.9990 overall best weight: 1.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 358 HIS B 129 ASN ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 212 ASN L 349 GLN ** L 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 358 HIS N 66 ASN N 129 ASN ** N 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 454 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5409 r_free = 0.5409 target = 0.288966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5116 r_free = 0.5116 target = 0.253090 restraints weight = 47239.880| |-----------------------------------------------------------------------------| r_work (start): 0.5079 rms_B_bonded: 2.86 r_work: 0.4926 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4779 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 32375 Z= 0.247 Angle : 0.747 22.917 44449 Z= 0.402 Chirality : 0.050 0.365 4901 Planarity : 0.006 0.088 5060 Dihedral : 18.595 178.981 5854 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.99 % Allowed : 14.47 % Favored : 83.53 % 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: -1.10 (0.14), residues: 3386 helix: 0.75 (0.16), residues: 1143 sheet: -0.38 (0.21), residues: 599 loop : -2.00 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 209 TYR 0.066 0.002 TYR I 210 PHE 0.037 0.003 PHE I 120 TRP 0.056 0.003 TRP M 369 HIS 0.012 0.002 HIS L 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.25 (32370) covalent geometry : angle 0.74712 / 0.40 (44449) hydrogen bonds : bond 0.05665 / 3.80 ( 1195) hydrogen bonds : angle 5.28349 / 3.68 ( 3388) Misc. bond : bond 0.00603 / 0.39 ( 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 314 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 253 time to evaluate : 1.061 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 211 LYS cc_start: 0.2827 (OUTLIER) cc_final: 0.2255 (mtmt) REVERT: A 277 MET cc_start: -0.1606 (mmm) cc_final: -0.1976 (mmm) REVERT: A 395 MET cc_start: 0.2410 (OUTLIER) cc_final: 0.0064 (tpp) REVERT: B 456 LEU cc_start: 0.1411 (OUTLIER) cc_final: 0.0682 (mp) REVERT: F 1 MET cc_start: 0.3537 (mmm) cc_final: 0.3040 (mmm) REVERT: F 223 ILE cc_start: 0.7468 (OUTLIER) cc_final: 0.7237 (mm) REVERT: F 364 ARG cc_start: 0.5443 (OUTLIER) cc_final: 0.3653 (mmm160) REVERT: F 407 ARG cc_start: 0.5743 (ttt180) cc_final: 0.5346 (ttt180) REVERT: F 435 MET cc_start: 0.0682 (mtt) cc_final: 0.0332 (mtt) REVERT: I 112 ILE cc_start: 0.2968 (pt) cc_final: 0.2612 (pt) REVERT: I 336 MET cc_start: 0.5137 (OUTLIER) cc_final: 0.4672 (mpt) REVERT: I 370 ASN cc_start: 0.4607 (OUTLIER) cc_final: 0.4201 (t0) REVERT: I 395 MET cc_start: 0.3701 (OUTLIER) cc_final: 0.3462 (pp-130) REVERT: M 126 ARG cc_start: 0.4640 (tpm170) cc_final: 0.4218 (tpm170) REVERT: N 19 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.6687 (mmtp) REVERT: N 25 ASP cc_start: 0.6474 (m-30) cc_final: 0.6207 (m-30) REVERT: N 452 ILE cc_start: 0.6508 (tp) cc_final: 0.6307 (tt) outliers start: 61 outliers final: 33 residues processed: 294 average time/residue: 0.4853 time to fit residues: 178.8169 Evaluate side-chains 283 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 241 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS 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 311 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 456 LEU 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 309 MET Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 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 78 LEU Chi-restraints excluded: chain I residue 210 TYR Chi-restraints excluded: chain I residue 336 MET Chi-restraints excluded: chain I residue 370 ASN Chi-restraints excluded: chain I residue 395 MET 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 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 265 ILE Chi-restraints excluded: chain N residue 19 LYS Chi-restraints excluded: chain N residue 41 SER 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 507 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 148 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 chunk 198 optimal weight: 4.9990 chunk 265 optimal weight: 0.7980 chunk 211 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 274 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 129 ASN ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN M 69 ASN M 358 HIS ** N 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5419 r_free = 0.5419 target = 0.290213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5129 r_free = 0.5129 target = 0.254807 restraints weight = 47225.085| |-----------------------------------------------------------------------------| r_work (start): 0.5096 rms_B_bonded: 2.89 r_work: 0.4953 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4725 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32375 Z= 0.173 Angle : 0.658 22.622 44449 Z= 0.352 Chirality : 0.046 0.318 4901 Planarity : 0.005 0.051 5060 Dihedral : 18.525 179.272 5854 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.89 % Allowed : 15.29 % Favored : 82.82 % 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: -0.94 (0.14), residues: 3386 helix: 0.98 (0.16), residues: 1142 sheet: -0.21 (0.22), residues: 593 loop : -2.01 (0.14), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG N 113 TYR 0.026 0.002 TYR I 210 PHE 0.036 0.002 PHE L 30 TRP 0.036 0.002 TRP F 86 HIS 0.008 0.001 HIS L 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (32370) covalent geometry : angle 0.65844 / 0.35 (44449) hydrogen bonds : bond 0.04601 / 3.06 ( 1195) hydrogen bonds : angle 5.05789 / 3.53 ( 3388) Misc. bond : bond 0.00542 / 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 310 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 252 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.2600 (OUTLIER) cc_final: 0.2129 (mtmt) REVERT: A 277 MET cc_start: -0.1689 (mmm) cc_final: -0.2339 (mmm) REVERT: A 395 MET cc_start: 0.2261 (OUTLIER) cc_final: 0.0140 (tmt) REVERT: B 6 TYR cc_start: 0.5064 (t80) cc_final: 0.4763 (t80) REVERT: B 456 LEU cc_start: 0.1270 (OUTLIER) cc_final: 0.1036 (mt) REVERT: F 1 MET cc_start: 0.3496 (mmm) cc_final: 0.2994 (mmm) REVERT: F 14 PHE cc_start: 0.5683 (m-80) cc_final: 0.4688 (m-80) REVERT: F 223 ILE cc_start: 0.7390 (OUTLIER) cc_final: 0.7159 (mm) REVERT: F 364 ARG cc_start: 0.5353 (OUTLIER) cc_final: 0.3541 (mmm160) REVERT: F 407 ARG cc_start: 0.5716 (ttt180) cc_final: 0.5390 (ttt180) REVERT: F 435 MET cc_start: 0.0563 (mtt) cc_final: 0.0210 (mtt) REVERT: I 112 ILE cc_start: 0.3201 (pt) cc_final: 0.2900 (OUTLIER) REVERT: I 135 PHE cc_start: 0.6130 (m-10) cc_final: 0.5683 (m-10) REVERT: I 336 MET cc_start: 0.5052 (OUTLIER) cc_final: 0.4579 (mpt) REVERT: I 370 ASN cc_start: 0.4593 (OUTLIER) cc_final: 0.4213 (t0) REVERT: L 320 TRP cc_start: 0.5050 (m100) cc_final: 0.4840 (m100) REVERT: N 19 LYS cc_start: 0.7494 (mtpm) cc_final: 0.6768 (mptt) REVERT: N 25 ASP cc_start: 0.6438 (m-30) cc_final: 0.6086 (m-30) REVERT: N 205 GLN cc_start: 0.6364 (mm-40) cc_final: 0.5510 (mm110) outliers start: 58 outliers final: 32 residues processed: 294 average time/residue: 0.4848 time to fit residues: 178.9073 Evaluate side-chains 281 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 243 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS 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 92 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 336 MET Chi-restraints excluded: chain I residue 370 ASN 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 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 41 SER 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 490 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 100 optimal weight: 4.9990 chunk 286 optimal weight: 0.3980 chunk 259 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 273 optimal weight: 2.9990 chunk 341 optimal weight: 0.0870 chunk 291 optimal weight: 3.9990 chunk 306 optimal weight: 1.9990 chunk 311 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 358 HIS N 329 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5424 r_free = 0.5424 target = 0.290926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5143 r_free = 0.5143 target = 0.255993 restraints weight = 47420.088| |-----------------------------------------------------------------------------| r_work (start): 0.5112 rms_B_bonded: 2.96 r_work: 0.4960 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4711 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 32375 Z= 0.149 Angle : 0.631 20.394 44449 Z= 0.339 Chirality : 0.045 0.309 4901 Planarity : 0.005 0.052 5060 Dihedral : 18.448 179.326 5854 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.50 % Allowed : 16.11 % Favored : 82.39 % 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: -0.85 (0.14), residues: 3386 helix: 1.12 (0.16), residues: 1137 sheet: -0.18 (0.22), residues: 602 loop : -2.01 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 364 TYR 0.014 0.001 TYR N 65 PHE 0.035 0.002 PHE L 30 TRP 0.093 0.002 TRP A 20 HIS 0.005 0.001 HIS B 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (32370) covalent geometry : angle 0.63087 / 0.34 (44449) hydrogen bonds : bond 0.04293 / 2.84 ( 1195) hydrogen bonds : angle 4.95809 / 3.47 ( 3388) Misc. bond : bond 0.00504 / 0.31 ( 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: 46 poor density : 244 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.2423 (OUTLIER) cc_final: 0.1795 (mtmt) REVERT: A 277 MET cc_start: -0.1579 (mmm) cc_final: -0.2526 (mmm) REVERT: A 395 MET cc_start: 0.2248 (OUTLIER) cc_final: 0.0117 (tmt) REVERT: F 1 MET cc_start: 0.3487 (mmm) cc_final: 0.2971 (mmm) REVERT: F 14 PHE cc_start: 0.5700 (m-80) cc_final: 0.4737 (m-80) REVERT: F 223 ILE cc_start: 0.7415 (OUTLIER) cc_final: 0.7198 (mm) REVERT: F 364 ARG cc_start: 0.5374 (OUTLIER) cc_final: 0.3543 (mmm160) REVERT: F 407 ARG cc_start: 0.5694 (ttt180) cc_final: 0.5337 (ttt180) REVERT: F 435 MET cc_start: 0.0641 (mtt) cc_final: 0.0287 (mtt) REVERT: I 112 ILE cc_start: 0.3144 (pt) cc_final: 0.2788 (pt) REVERT: I 135 PHE cc_start: 0.6181 (m-10) cc_final: 0.5719 (m-10) REVERT: I 210 TYR cc_start: 0.4537 (t80) cc_final: 0.4266 (t80) REVERT: I 336 MET cc_start: 0.4984 (OUTLIER) cc_final: 0.4509 (mpt) REVERT: I 370 ASN cc_start: 0.4638 (OUTLIER) cc_final: 0.4246 (t0) REVERT: L 14 PHE cc_start: 0.6122 (m-80) cc_final: 0.5434 (m-80) REVERT: L 139 TRP cc_start: 0.5887 (m100) cc_final: 0.5459 (t-100) REVERT: N 19 LYS cc_start: 0.7483 (mtpm) cc_final: 0.6767 (mptt) REVERT: N 25 ASP cc_start: 0.6432 (m-30) cc_final: 0.6139 (m-30) REVERT: N 205 GLN cc_start: 0.6259 (mm-40) cc_final: 0.5483 (mm110) outliers start: 46 outliers final: 32 residues processed: 277 average time/residue: 0.4885 time to fit residues: 169.9153 Evaluate side-chains 278 residues out of total 3061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 240 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 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 123 SER Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 459 ILE 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 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 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 74 VAL Chi-restraints excluded: chain N residue 41 SER 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 429 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: 3.9990 chunk 63 optimal weight: 0.5980 chunk 218 optimal weight: 0.6980 chunk 124 optimal weight: 0.0010 chunk 185 optimal weight: 1.9990 chunk 320 optimal weight: 0.0980 chunk 331 optimal weight: 1.9990 chunk 223 optimal weight: 6.9990 chunk 281 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 358 HIS N 217 HIS 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 = 0.291587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5160 r_free = 0.5160 target = 0.257592 restraints weight = 47593.875| |-----------------------------------------------------------------------------| r_work (start): 0.5128 rms_B_bonded: 2.87 r_work: 0.4967 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4694 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 32375 Z= 0.137 Angle : 0.622 19.072 44449 Z= 0.333 Chirality : 0.044 0.294 4901 Planarity : 0.004 0.050 5060 Dihedral : 18.388 179.748 5854 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.47 % Allowed : 16.17 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z 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: -0.76 (0.14), residues: 3386 helix: 1.19 (0.16), residues: 1141 sheet: -0.09 (0.22), residues: 602 loop : -1.98 (0.14), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 481 TYR 0.028 0.001 TYR B 6 PHE 0.032 0.002 PHE L 30 TRP 0.128 0.002 TRP A 20 HIS 0.005 0.001 HIS B 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (32370) covalent geometry : angle 0.62164 / 0.33 (44449) hydrogen bonds : bond 0.04039 / 2.67 ( 1195) hydrogen bonds : angle 4.85407 / 3.41 ( 3388) Misc. bond : bond 0.00468 / 0.29 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11279.72 seconds wall clock time: 192 minutes 53.71 seconds (11573.71 seconds total)