Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 13 14:42:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyf_32203/07_2023/7vyf_32203_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyf_32203/07_2023/7vyf_32203.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyf_32203/07_2023/7vyf_32203_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyf_32203/07_2023/7vyf_32203_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyf_32203/07_2023/7vyf_32203_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyf_32203/07_2023/7vyf_32203.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyf_32203/07_2023/7vyf_32203.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyf_32203/07_2023/7vyf_32203_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyf_32203/07_2023/7vyf_32203_updated.pdb" } resolution = 2.8 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.005 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: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 8 5.49 5 Mg 1 5.21 5 S 189 5.16 5 C 18039 2.51 5 N 4952 2.21 5 O 5238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 217": "OE1" <-> "OE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A ARG 398": "NH1" <-> "NH2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H GLU 79": "OE1" <-> "OE2" Residue "J GLU 133": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J GLU 234": "OE1" <-> "OE2" Residue "J TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 139": "OE1" <-> "OE2" Residue "M GLU 535": "OE1" <-> "OE2" Residue "M PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 660": "OE1" <-> "OE2" Residue "O GLU 150": "OE1" <-> "OE2" Residue "O GLU 194": "OE1" <-> "OE2" Residue "P ASP 183": "OD1" <-> "OD2" Residue "P GLU 209": "OE1" <-> "OE2" Residue "Q GLU 370": "OE1" <-> "OE2" Residue "T GLU 78": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 28456 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3330 Classifications: {'peptide': 433} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 410} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 687 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2751 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 22, 'TRANS': 319} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 366 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1667 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3096 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 364} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "W" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 23} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'970': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 128 Unusual residues: {' UQ': 1, 'NDP': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 30 Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2718 SG CYS A 382 47.257 48.229 105.077 1.00 15.01 S ATOM 3060 SG CYS A 425 46.622 45.117 110.919 1.00 16.83 S ATOM 2738 SG CYS A 385 44.196 43.832 105.072 1.00 16.21 S ATOM 2699 SG CYS A 379 41.824 48.654 108.944 1.00 17.60 S ATOM 3961 SG CYS B 113 35.464 63.636 70.197 1.00 12.98 S ATOM 3980 SG CYS B 116 40.715 61.482 73.979 1.00 11.73 S ATOM 4003 SG CYS B 119 41.613 64.328 68.624 1.00 12.27 S ATOM 4332 SG CYS B 162 39.351 58.367 69.163 1.00 9.94 S ATOM 4030 SG CYS B 123 47.455 67.267 64.122 1.00 10.95 S ATOM 4256 SG CYS B 152 46.046 65.469 58.105 1.00 5.69 S ATOM 4303 SG CYS B 158 44.113 61.627 63.054 1.00 9.68 S ATOM 4282 SG CYS B 155 50.231 62.277 61.417 1.00 5.92 S ATOM 5724 SG CYS C 166 52.663 65.769 53.890 1.00 9.77 S ATOM 4996 SG CYS C 72 52.908 67.339 47.688 1.00 12.75 S ATOM 4990 SG CYS C 71 58.370 65.648 50.907 1.00 13.76 S ATOM 5494 SG CYS C 136 54.802 70.931 52.810 1.00 11.36 S ATOM 14949 SG CYS M 131 39.747 61.615 86.074 1.00 10.93 S ATOM 14928 SG CYS M 128 43.623 57.082 83.015 1.00 9.94 S ATOM 14989 SG CYS M 137 45.466 60.681 88.228 1.00 11.40 S ATOM 15321 SG CYS M 179 43.708 60.774 99.286 1.00 12.87 S ATOM 15675 SG CYS M 226 40.494 63.364 94.971 1.00 12.78 S ATOM 15345 SG CYS M 182 38.043 63.245 101.059 1.00 13.88 S ATOM 15298 SG CYS M 176 38.192 57.810 97.586 1.00 12.01 S ATOM 14546 SG CYS M 78 55.525 56.872 103.149 1.00 13.43 S ATOM 14647 SG CYS M 92 53.604 58.856 105.392 1.00 15.58 S ATOM 14435 SG CYS M 64 49.165 58.477 103.130 1.00 11.92 S ATOM 14521 SG CYS M 75 50.296 56.594 100.226 1.00 12.13 S ATOM 21484 SG CYS O 135 31.810 30.116 113.050 1.00 38.13 S ATOM 21518 SG CYS O 140 31.110 26.653 113.504 1.00 40.30 S ATOM 21798 SG CYS O 176 35.968 31.438 115.559 1.00 36.59 S ATOM 21821 SG CYS O 180 36.631 28.355 116.257 1.00 43.05 S ATOM 27627 SG CYS T 86 28.723 49.954 77.935 1.00 23.13 S ATOM 27805 SG CYS T 111 29.750 53.383 79.081 1.00 25.69 S Time building chain proxies: 14.03, per 1000 atoms: 0.49 Number of scatterers: 28456 At special positions: 0 Unit cell: (124.607, 142.869, 161.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 189 16.00 P 8 15.00 Mg 1 11.99 O 5238 8.00 N 4952 7.00 C 18039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.39 Conformation dependent library (CDL) restraints added in 4.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb=" SF4 A 501 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb=" SF4 C 301 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb=" SF4 M 802 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 155 helices and 25 sheets defined 38.9% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 95 through 102 removed outlier: 3.528A pdb=" N PHE A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N MET A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 363 through 377 Processing helix chain 'A' and resid 383 through 401 removed outlier: 4.532A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 4.025A pdb=" N ASP A 410 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 441 Proline residue: A 434 - end of helix Processing helix chain 'A' and resid 443 through 457 Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.640A pdb=" N PHE B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 180 through 183 Processing helix chain 'B' and resid 187 through 206 removed outlier: 5.645A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 71 through 79 removed outlier: 3.898A pdb=" N GLU C 75 " --> pdb=" O CYS C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 114 through 122 Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'E' and resid 25 through 50 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.214A pdb=" N ASN E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 106 removed outlier: 4.422A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 39 removed outlier: 4.912A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 47 Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 95 Processing helix chain 'G' and resid 76 through 88 Processing helix chain 'G' and resid 95 through 97 No H-bonds generated for 'chain 'G' and resid 95 through 97' Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 3.890A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'H' and resid 78 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 54 through 56 No H-bonds generated for 'chain 'I' and resid 54 through 56' Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 64 through 76 removed outlier: 4.130A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 5.098A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 214 through 223 removed outlier: 3.658A pdb=" N MET J 220 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARG J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N TRP J 222 " --> pdb=" O ALA J 218 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N PHE J 223 " --> pdb=" O SER J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 232 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 295 through 307 removed outlier: 3.999A pdb=" N VAL J 307 " --> pdb=" O ARG J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 322 Processing helix chain 'J' and resid 336 through 338 No H-bonds generated for 'chain 'J' and resid 336 through 338' Processing helix chain 'J' and resid 345 through 347 No H-bonds generated for 'chain 'J' and resid 345 through 347' Processing helix chain 'J' and resid 350 through 353 No H-bonds generated for 'chain 'J' and resid 350 through 353' Processing helix chain 'J' and resid 359 through 361 No H-bonds generated for 'chain 'J' and resid 359 through 361' Processing helix chain 'J' and resid 366 through 368 No H-bonds generated for 'chain 'J' and resid 366 through 368' Processing helix chain 'K' and resid 77 through 79 No H-bonds generated for 'chain 'K' and resid 77 through 79' Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.477A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 69 through 73 removed outlier: 4.453A pdb=" N LYS L 73 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 94 No H-bonds generated for 'chain 'L' and resid 92 through 94' Processing helix chain 'L' and resid 131 through 141 Processing helix chain 'L' and resid 161 through 164 Processing helix chain 'M' and resid 49 through 56 removed outlier: 3.765A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 128 through 130 No H-bonds generated for 'chain 'M' and resid 128 through 130' Processing helix chain 'M' and resid 138 through 146 Processing helix chain 'M' and resid 173 through 175 No H-bonds generated for 'chain 'M' and resid 173 through 175' Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 201 through 203 No H-bonds generated for 'chain 'M' and resid 201 through 203' Processing helix chain 'M' and resid 219 through 225 removed outlier: 3.729A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 292 Processing helix chain 'M' and resid 295 through 298 Processing helix chain 'M' and resid 319 through 332 Processing helix chain 'M' and resid 335 through 337 No H-bonds generated for 'chain 'M' and resid 335 through 337' Processing helix chain 'M' and resid 348 through 360 Processing helix chain 'M' and resid 382 through 385 removed outlier: 3.598A pdb=" N TYR M 385 " --> pdb=" O ARG M 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 382 through 385' Processing helix chain 'M' and resid 390 through 396 removed outlier: 3.716A pdb=" N VAL M 394 " --> pdb=" O THR M 390 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU M 395 " --> pdb=" O ILE M 391 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU M 396 " --> pdb=" O ALA M 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 390 through 396' Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 424 Processing helix chain 'M' and resid 449 through 457 Processing helix chain 'M' and resid 461 through 468 Processing helix chain 'M' and resid 478 through 482 Processing helix chain 'M' and resid 486 through 504 Processing helix chain 'M' and resid 522 through 527 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 557 through 559 No H-bonds generated for 'chain 'M' and resid 557 through 559' Processing helix chain 'M' and resid 589 through 591 No H-bonds generated for 'chain 'M' and resid 589 through 591' Processing helix chain 'M' and resid 619 through 630 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 654 Processing helix chain 'M' and resid 665 through 673 Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 17 removed outlier: 3.641A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 30 Processing helix chain 'N' and resid 79 through 81 No H-bonds generated for 'chain 'N' and resid 79 through 81' Processing helix chain 'N' and resid 84 through 90 Processing helix chain 'O' and resid 57 through 69 removed outlier: 3.841A pdb=" N ASN O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 90 removed outlier: 4.636A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 141 No H-bonds generated for 'chain 'O' and resid 138 through 141' Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 198 through 209 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 4.880A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix Processing helix chain 'P' and resid 161 through 174 removed outlier: 3.923A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU P 167 " --> pdb=" O ASN P 164 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET P 173 " --> pdb=" O ILE P 170 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE P 174 " --> pdb=" O TRP P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 245 No H-bonds generated for 'chain 'P' and resid 243 through 245' Processing helix chain 'Q' and resid 89 through 91 No H-bonds generated for 'chain 'Q' and resid 89 through 91' Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.737A pdb=" N TYR Q 126 " --> pdb=" O LYS Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 139 removed outlier: 3.910A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 159 Processing helix chain 'Q' and resid 165 through 194 Processing helix chain 'Q' and resid 198 through 218 removed outlier: 3.853A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 248 Processing helix chain 'Q' and resid 251 through 262 Processing helix chain 'Q' and resid 266 through 272 Processing helix chain 'Q' and resid 280 through 285 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.320A pdb=" N GLY Q 295 " --> pdb=" O MET Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 305 No H-bonds generated for 'chain 'Q' and resid 302 through 305' Processing helix chain 'Q' and resid 310 through 313 Processing helix chain 'Q' and resid 326 through 349 Processing helix chain 'Q' and resid 368 through 373 Processing helix chain 'Q' and resid 375 through 386 Processing helix chain 'Q' and resid 427 through 438 removed outlier: 4.533A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 453 Processing helix chain 'Q' and resid 458 through 462 Processing helix chain 'T' and resid 50 through 55 Processing helix chain 'T' and resid 67 through 72 removed outlier: 3.546A pdb=" N ALA T 72 " --> pdb=" O ILE T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing sheet with id= A, first strand: chain 'A' and resid 239 through 244 removed outlier: 6.376A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 5.998A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N THR B 142 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 102 through 106 removed outlier: 6.621A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE C 161 " --> pdb=" O SER C 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 52 through 58 removed outlier: 6.846A pdb=" N ARG F 68 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE F 19 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TRP F 66 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE F 21 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS F 64 " --> pdb=" O ILE F 21 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.572A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 226 through 228 Processing sheet with id= I, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= J, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= K, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= L, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= N, first strand: chain 'M' and resid 246 through 251 removed outlier: 6.166A pdb=" N ARG M 266 " --> pdb=" O VAL M 270 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL M 270 " --> pdb=" O ARG M 266 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= P, first strand: chain 'M' and resid 338 through 342 removed outlier: 6.271A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'M' and resid 428 through 432 Processing sheet with id= R, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= S, first strand: chain 'N' and resid 60 through 63 removed outlier: 6.617A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.397A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.849A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= W, first strand: chain 'Q' and resid 80 through 84 removed outlier: 6.267A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= Y, first strand: chain 'T' and resid 83 through 86 926 hydrogen bonds defined for protein. 2511 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.75 Time building geometry restraints manager: 12.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 11760 1.40 - 1.62: 17020 1.62 - 1.84: 272 1.84 - 2.06: 1 2.06 - 2.28: 80 Bond restraints: 29133 Sorted by residual: bond pdb=" C18 UQ J 403 " pdb=" C19 UQ J 403 " ideal model delta sigma weight residual 1.336 1.556 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C13 UQ J 403 " pdb=" C14 UQ J 403 " ideal model delta sigma weight residual 1.335 1.548 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C17 970 C 302 " pdb=" O16 970 C 302 " ideal model delta sigma weight residual 1.355 1.568 -0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C23 UQ J 403 " pdb=" C24 UQ J 403 " ideal model delta sigma weight residual 1.335 1.545 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C8 UQ J 403 " pdb=" C9 UQ J 403 " ideal model delta sigma weight residual 1.334 1.536 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 29128 not shown) Histogram of bond angle deviations from ideal: 73.53 - 85.72: 76 85.72 - 97.91: 1 97.91 - 110.10: 5088 110.10 - 122.29: 29793 122.29 - 134.48: 4532 Bond angle restraints: 39490 Sorted by residual: angle pdb=" PA NDP J 402 " pdb=" O3 NDP J 402 " pdb=" PN NDP J 402 " ideal model delta sigma weight residual 107.74 124.79 -17.05 1.95e+00 2.62e-01 7.62e+01 angle pdb=" C11 CDL N 201 " pdb=" CA5 CDL N 201 " pdb=" OA6 CDL N 201 " ideal model delta sigma weight residual 111.33 120.73 -9.40 1.32e+00 5.72e-01 5.05e+01 angle pdb=" C5B NDP J 402 " pdb=" O5B NDP J 402 " pdb=" PA NDP J 402 " ideal model delta sigma weight residual 103.84 117.35 -13.51 1.91e+00 2.73e-01 4.98e+01 angle pdb=" C51 CDL N 201 " pdb=" CB5 CDL N 201 " pdb=" OB6 CDL N 201 " ideal model delta sigma weight residual 111.33 120.47 -9.14 1.32e+00 5.72e-01 4.78e+01 angle pdb=" O1X NDP J 402 " pdb=" P2B NDP J 402 " pdb=" O3X NDP J 402 " ideal model delta sigma weight residual 117.46 109.44 8.02 1.17e+00 7.36e-01 4.73e+01 ... (remaining 39485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.58: 17176 33.58 - 67.15: 325 67.15 - 100.72: 44 100.72 - 134.30: 2 134.30 - 167.87: 1 Dihedral angle restraints: 17548 sinusoidal: 7319 harmonic: 10229 Sorted by residual: dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual -102.41 65.47 -167.87 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" CB CYS F 24 " pdb=" SG CYS F 24 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual 93.00 40.93 52.07 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CA LEU I 106 " pdb=" C LEU I 106 " pdb=" N SER I 107 " pdb=" CA SER I 107 " ideal model delta harmonic sigma weight residual 180.00 154.68 25.32 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 17545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3861 0.077 - 0.153: 400 0.153 - 0.230: 10 0.230 - 0.306: 3 0.306 - 0.383: 1 Chirality restraints: 4275 Sorted by residual: chirality pdb=" C3B NDP J 402 " pdb=" C2B NDP J 402 " pdb=" C4B NDP J 402 " pdb=" O3B NDP J 402 " both_signs ideal model delta sigma weight residual False -2.75 -2.36 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CA PHE B 78 " pdb=" N PHE B 78 " pdb=" C PHE B 78 " pdb=" CB PHE B 78 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C3D NDP J 402 " pdb=" C2D NDP J 402 " pdb=" C4D NDP J 402 " pdb=" O3D NDP J 402 " both_signs ideal model delta sigma weight residual False -2.71 -2.44 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 4272 not shown) Planarity restraints: 5091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ J 403 " -0.109 2.00e-02 2.50e+03 2.60e-01 8.44e+02 pdb=" C11 UQ J 403 " 0.061 2.00e-02 2.50e+03 pdb=" C7 UQ J 403 " 0.236 2.00e-02 2.50e+03 pdb=" C8 UQ J 403 " -0.446 2.00e-02 2.50e+03 pdb=" C9 UQ J 403 " 0.259 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ J 403 " -0.201 2.00e-02 2.50e+03 2.27e-01 6.44e+02 pdb=" C13 UQ J 403 " 0.142 2.00e-02 2.50e+03 pdb=" C14 UQ J 403 " 0.356 2.00e-02 2.50e+03 pdb=" C15 UQ J 403 " -0.034 2.00e-02 2.50e+03 pdb=" C16 UQ J 403 " -0.263 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP J 402 " 0.068 2.00e-02 2.50e+03 2.26e-01 6.39e+02 pdb=" C3N NDP J 402 " 0.403 2.00e-02 2.50e+03 pdb=" C4N NDP J 402 " -0.071 2.00e-02 2.50e+03 pdb=" C7N NDP J 402 " -0.245 2.00e-02 2.50e+03 pdb=" N1N NDP J 402 " -0.154 2.00e-02 2.50e+03 ... (remaining 5088 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 362 2.64 - 3.21: 25420 3.21 - 3.77: 44878 3.77 - 4.34: 66916 4.34 - 4.90: 106394 Nonbonded interactions: 243970 Sorted by model distance: nonbonded pdb=" N1 FMN A 502 " pdb=" O3' FMN A 502 " model vdw 2.078 2.520 nonbonded pdb=" NH2 ARG A 152 " pdb=" O PRO K 99 " model vdw 2.207 2.520 nonbonded pdb=" O THR M 389 " pdb=" OG1 THR M 390 " model vdw 2.211 2.440 nonbonded pdb=" OH TYR N 127 " pdb=" O GLU T 61 " model vdw 2.216 2.440 nonbonded pdb=" OG1 THR J 199 " pdb=" O ALA J 258 " model vdw 2.217 2.440 ... (remaining 243965 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.820 Check model and map are aligned: 0.420 Set scattering table: 0.270 Process input model: 79.990 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 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 0.315 29133 Z= 0.488 Angle : 0.753 17.055 39490 Z= 0.384 Chirality : 0.046 0.383 4275 Planarity : 0.010 0.260 5091 Dihedral : 13.891 167.874 10969 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.94 % Favored : 96.00 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3502 helix: 0.67 (0.14), residues: 1345 sheet: -0.07 (0.25), residues: 397 loop : -0.66 (0.14), residues: 1760 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 459 time to evaluate : 3.484 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 460 average time/residue: 1.7458 time to fit residues: 913.3881 Evaluate side-chains 379 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 378 time to evaluate : 3.409 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 4.4827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 291 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 89 optimal weight: 0.0020 chunk 176 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 270 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 201 optimal weight: 8.9990 chunk 313 optimal weight: 1.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN B 59 GLN F 76 ASN F 93 ASN ** J 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN M 464 GLN M 666 GLN M 669 ASN N 116 ASN O 41 HIS O 69 ASN O 123 ASN O 187 GLN P 247 GLN Q 92 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.0633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 29133 Z= 0.188 Angle : 0.529 12.680 39490 Z= 0.269 Chirality : 0.042 0.144 4275 Planarity : 0.004 0.055 5091 Dihedral : 7.750 174.663 4010 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.48 % Favored : 96.46 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3502 helix: 0.80 (0.14), residues: 1354 sheet: -0.01 (0.25), residues: 397 loop : -0.63 (0.15), residues: 1751 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 395 time to evaluate : 3.722 Fit side-chains outliers start: 38 outliers final: 14 residues processed: 412 average time/residue: 1.7390 time to fit residues: 818.0407 Evaluate side-chains 393 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 379 time to evaluate : 3.225 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 6 residues processed: 8 average time/residue: 0.3944 time to fit residues: 9.2418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 174 optimal weight: 0.0470 chunk 97 optimal weight: 0.4980 chunk 260 optimal weight: 0.8980 chunk 213 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 313 optimal weight: 1.9990 chunk 339 optimal weight: 4.9990 chunk 279 optimal weight: 0.9980 chunk 311 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 251 optimal weight: 0.0170 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN ** J 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 464 GLN M 666 GLN M 688 GLN N 116 ASN N 135 GLN O 187 GLN P 247 GLN Q 92 HIS Q 431 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.066 29133 Z= 0.138 Angle : 0.486 10.504 39490 Z= 0.247 Chirality : 0.041 0.145 4275 Planarity : 0.004 0.051 5091 Dihedral : 7.277 176.125 4010 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.51 % Favored : 96.46 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 3502 helix: 1.03 (0.14), residues: 1353 sheet: 0.09 (0.25), residues: 406 loop : -0.56 (0.15), residues: 1743 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 402 time to evaluate : 3.978 Fit side-chains outliers start: 42 outliers final: 16 residues processed: 420 average time/residue: 1.7275 time to fit residues: 829.8394 Evaluate side-chains 393 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 377 time to evaluate : 3.181 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 7 residues processed: 9 average time/residue: 0.4752 time to fit residues: 11.2623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 310 optimal weight: 2.9990 chunk 235 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 314 optimal weight: 5.9990 chunk 333 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 298 optimal weight: 5.9990 chunk 89 optimal weight: 0.0980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN F 76 ASN ** J 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 464 GLN M 540 ASN N 116 ASN O 41 HIS P 75 GLN Q 92 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 29133 Z= 0.279 Angle : 0.554 10.743 39490 Z= 0.282 Chirality : 0.044 0.146 4275 Planarity : 0.005 0.052 5091 Dihedral : 7.293 175.101 4010 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.71 % Favored : 96.26 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3502 helix: 0.86 (0.14), residues: 1353 sheet: 0.13 (0.25), residues: 405 loop : -0.60 (0.15), residues: 1744 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 379 time to evaluate : 3.273 Fit side-chains outliers start: 51 outliers final: 23 residues processed: 403 average time/residue: 1.7764 time to fit residues: 818.2244 Evaluate side-chains 391 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 368 time to evaluate : 3.273 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 10 residues processed: 14 average time/residue: 0.4419 time to fit residues: 13.6491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 277 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 284 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 299 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN F 76 ASN M 464 GLN M 598 ASN N 116 ASN N 135 GLN O 41 HIS Q 92 HIS T 43 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 29133 Z= 0.224 Angle : 0.524 10.594 39490 Z= 0.268 Chirality : 0.043 0.144 4275 Planarity : 0.004 0.055 5091 Dihedral : 7.170 175.488 4010 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.34 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3502 helix: 0.84 (0.14), residues: 1356 sheet: 0.11 (0.25), residues: 403 loop : -0.58 (0.15), residues: 1743 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 377 time to evaluate : 3.746 Fit side-chains outliers start: 44 outliers final: 23 residues processed: 397 average time/residue: 1.8074 time to fit residues: 823.1195 Evaluate side-chains 396 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 373 time to evaluate : 3.653 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 10 residues processed: 13 average time/residue: 0.6527 time to fit residues: 16.4141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 112 optimal weight: 2.9990 chunk 300 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 333 optimal weight: 4.9990 chunk 277 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN F 76 ASN J 79 GLN L 86 ASN M 598 ASN N 116 ASN N 122 GLN O 41 HIS Q 92 HIS Q 147 ASN Q 454 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.091 29133 Z= 0.392 Angle : 0.611 11.050 39490 Z= 0.313 Chirality : 0.047 0.155 4275 Planarity : 0.005 0.057 5091 Dihedral : 7.385 174.192 4010 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.97 % Favored : 95.97 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3502 helix: 0.58 (0.14), residues: 1355 sheet: 0.06 (0.25), residues: 409 loop : -0.70 (0.14), residues: 1738 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 371 time to evaluate : 3.353 Fit side-chains outliers start: 57 outliers final: 28 residues processed: 401 average time/residue: 1.7604 time to fit residues: 804.7326 Evaluate side-chains 393 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 365 time to evaluate : 3.615 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 16 residues processed: 12 average time/residue: 0.6015 time to fit residues: 14.8006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 321 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 243 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 280 optimal weight: 0.8980 chunk 186 optimal weight: 0.7980 chunk 332 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 153 optimal weight: 0.2980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN F 76 ASN L 86 ASN M 666 GLN N 122 GLN N 135 GLN O 41 HIS P 247 GLN Q 92 HIS T 43 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 29133 Z= 0.192 Angle : 0.521 10.824 39490 Z= 0.266 Chirality : 0.042 0.143 4275 Planarity : 0.004 0.057 5091 Dihedral : 7.079 176.082 4010 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.63 % Favored : 96.32 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3502 helix: 0.77 (0.14), residues: 1357 sheet: 0.08 (0.25), residues: 403 loop : -0.61 (0.15), residues: 1742 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 383 time to evaluate : 3.632 Fit side-chains outliers start: 51 outliers final: 30 residues processed: 410 average time/residue: 1.7876 time to fit residues: 840.4345 Evaluate side-chains 399 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 369 time to evaluate : 3.659 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 18 residues processed: 12 average time/residue: 0.9539 time to fit residues: 19.5221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 205 optimal weight: 0.0970 chunk 132 optimal weight: 0.1980 chunk 198 optimal weight: 2.9990 chunk 100 optimal weight: 0.0070 chunk 65 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 211 optimal weight: 6.9990 chunk 226 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 261 optimal weight: 4.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN F 76 ASN L 86 ASN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 666 GLN N 116 ASN N 122 GLN O 99 ASN P 247 GLN Q 92 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.067 29133 Z= 0.129 Angle : 0.486 11.562 39490 Z= 0.247 Chirality : 0.041 0.139 4275 Planarity : 0.004 0.052 5091 Dihedral : 6.716 177.570 4010 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.34 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3502 helix: 1.05 (0.14), residues: 1353 sheet: 0.08 (0.25), residues: 418 loop : -0.49 (0.15), residues: 1731 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 390 time to evaluate : 3.463 Fit side-chains outliers start: 33 outliers final: 18 residues processed: 413 average time/residue: 1.7485 time to fit residues: 826.3521 Evaluate side-chains 386 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 368 time to evaluate : 3.412 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 2 average time/residue: 0.8830 time to fit residues: 6.8062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 302 optimal weight: 0.6980 chunk 318 optimal weight: 5.9990 chunk 290 optimal weight: 1.9990 chunk 309 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 243 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 280 optimal weight: 2.9990 chunk 293 optimal weight: 3.9990 chunk 308 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN F 76 ASN L 86 ASN M 666 GLN N 116 ASN N 122 GLN O 41 HIS O 153 GLN Q 92 HIS Q 147 ASN T 43 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 29133 Z= 0.249 Angle : 0.554 15.338 39490 Z= 0.281 Chirality : 0.043 0.144 4275 Planarity : 0.005 0.053 5091 Dihedral : 6.855 175.905 4010 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.34 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.14), residues: 3502 helix: 0.90 (0.14), residues: 1357 sheet: 0.12 (0.25), residues: 407 loop : -0.50 (0.15), residues: 1738 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 371 time to evaluate : 3.650 Fit side-chains outliers start: 35 outliers final: 21 residues processed: 394 average time/residue: 1.7882 time to fit residues: 809.2215 Evaluate side-chains 387 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 366 time to evaluate : 3.843 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 17 residues processed: 4 average time/residue: 0.8142 time to fit residues: 9.0675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 203 optimal weight: 2.9990 chunk 327 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 227 optimal weight: 0.7980 chunk 343 optimal weight: 0.8980 chunk 316 optimal weight: 1.9990 chunk 273 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 211 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN F 76 ASN L 86 ASN M 666 GLN N 122 GLN O 41 HIS P 63 GLN Q 92 HIS Q 147 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 29133 Z= 0.166 Angle : 0.510 11.560 39490 Z= 0.259 Chirality : 0.042 0.140 4275 Planarity : 0.004 0.054 5091 Dihedral : 6.673 177.101 4010 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.54 % Favored : 96.43 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3502 helix: 1.02 (0.14), residues: 1353 sheet: 0.15 (0.25), residues: 414 loop : -0.51 (0.15), residues: 1735 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 376 time to evaluate : 3.327 Fit side-chains outliers start: 27 outliers final: 19 residues processed: 396 average time/residue: 1.7488 time to fit residues: 795.8420 Evaluate side-chains 392 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 373 time to evaluate : 3.607 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 0.4691 time to fit residues: 6.2510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 217 optimal weight: 2.9990 chunk 291 optimal weight: 0.3980 chunk 83 optimal weight: 0.0970 chunk 252 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 274 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 281 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 0.0670 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN F 76 ASN H 71 GLN L 86 ASN M 666 GLN N 116 ASN N 122 GLN P 63 GLN Q 92 HIS T 43 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.117656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.095287 restraints weight = 35377.877| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.26 r_work: 0.2839 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 29133 Z= 0.137 Angle : 0.496 16.868 39490 Z= 0.250 Chirality : 0.041 0.139 4275 Planarity : 0.004 0.051 5091 Dihedral : 6.479 177.949 4010 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.57 % Favored : 96.40 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.14), residues: 3502 helix: 1.21 (0.14), residues: 1340 sheet: 0.19 (0.25), residues: 414 loop : -0.45 (0.15), residues: 1748 =============================================================================== Job complete usr+sys time: 11773.26 seconds wall clock time: 210 minutes 2.63 seconds (12602.63 seconds total)