Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 13:31:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz6_22530/10_2023/7jz6_22530_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz6_22530/10_2023/7jz6_22530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz6_22530/10_2023/7jz6_22530.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz6_22530/10_2023/7jz6_22530.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz6_22530/10_2023/7jz6_22530_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz6_22530/10_2023/7jz6_22530_updated.pdb" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.360 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: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 44 5.16 5 C 13258 2.51 5 N 3589 2.21 5 O 3947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 52": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A ARG 112": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 381": "NH1" <-> "NH2" Residue "A GLU 385": "OE1" <-> "OE2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A ARG 406": "NH1" <-> "NH2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A ARG 484": "NH1" <-> "NH2" Residue "A ARG 491": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 508": "NH1" <-> "NH2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A ARG 556": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A GLU 570": "OE1" <-> "OE2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A ARG 585": "NH1" <-> "NH2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A GLU 608": "OE1" <-> "OE2" Residue "A ARG 617": "NH1" <-> "NH2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A ARG 650": "NH1" <-> "NH2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 664": "OE1" <-> "OE2" Residue "A ARG 666": "NH1" <-> "NH2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A GLU 695": "OE1" <-> "OE2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A ARG 722": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B ARG 112": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B GLU 337": "OE1" <-> "OE2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B GLU 351": "OE1" <-> "OE2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ARG 381": "NH1" <-> "NH2" Residue "B GLU 385": "OE1" <-> "OE2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B ARG 406": "NH1" <-> "NH2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B ARG 421": "NH1" <-> "NH2" Residue "B GLU 447": "OE1" <-> "OE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B ARG 479": "NH1" <-> "NH2" Residue "B ARG 484": "NH1" <-> "NH2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B ARG 508": "NH1" <-> "NH2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B ARG 556": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B GLU 567": "OE1" <-> "OE2" Residue "B ARG 580": "NH1" <-> "NH2" Residue "B ARG 583": "NH1" <-> "NH2" Residue "B ARG 585": "NH1" <-> "NH2" Residue "B GLU 592": "OE1" <-> "OE2" Residue "B GLU 608": "OE1" <-> "OE2" Residue "B ARG 617": "NH1" <-> "NH2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B ARG 650": "NH1" <-> "NH2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B ARG 666": "NH1" <-> "NH2" Residue "B ARG 668": "NH1" <-> "NH2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B ARG 691": "NH1" <-> "NH2" Residue "B GLU 695": "OE1" <-> "OE2" Residue "B GLU 704": "OE1" <-> "OE2" Residue "B ARG 722": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C ARG 112": "NH1" <-> "NH2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C GLU 331": "OE1" <-> "OE2" Residue "C ARG 342": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 381": "NH1" <-> "NH2" Residue "C GLU 387": "OE1" <-> "OE2" Residue "C ARG 391": "NH1" <-> "NH2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "C ARG 406": "NH1" <-> "NH2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C ARG 421": "NH1" <-> "NH2" Residue "C GLU 447": "OE1" <-> "OE2" Residue "C ARG 479": "NH1" <-> "NH2" Residue "C ARG 484": "NH1" <-> "NH2" Residue "C ARG 491": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C ARG 508": "NH1" <-> "NH2" Residue "C ARG 556": "NH1" <-> "NH2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "C GLU 570": "OE1" <-> "OE2" Residue "C ARG 580": "NH1" <-> "NH2" Residue "C ARG 583": "NH1" <-> "NH2" Residue "C ARG 585": "NH1" <-> "NH2" Residue "C GLU 592": "OE1" <-> "OE2" Residue "C GLU 608": "OE1" <-> "OE2" Residue "C ARG 617": "NH1" <-> "NH2" Residue "C ARG 634": "NH1" <-> "NH2" Residue "C ARG 650": "NH1" <-> "NH2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C ARG 666": "NH1" <-> "NH2" Residue "C ARG 668": "NH1" <-> "NH2" Residue "C GLU 669": "OE1" <-> "OE2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C ARG 691": "NH1" <-> "NH2" Residue "C GLU 695": "OE1" <-> "OE2" Residue "C GLU 704": "OE1" <-> "OE2" Residue "C ARG 722": "NH1" <-> "NH2" Residue "D ARG 42": "NH1" <-> "NH2" Residue "D ARG 52": "NH1" <-> "NH2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D ARG 112": "NH1" <-> "NH2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "D GLU 190": "OE1" <-> "OE2" Residue "D GLU 230": "OE1" <-> "OE2" Residue "D ARG 246": "NH1" <-> "NH2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D GLU 291": "OE1" <-> "OE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "D GLU 337": "OE1" <-> "OE2" Residue "D ARG 342": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ARG 381": "NH1" <-> "NH2" Residue "D GLU 387": "OE1" <-> "OE2" Residue "D ARG 391": "NH1" <-> "NH2" Residue "D ARG 392": "NH1" <-> "NH2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D ARG 406": "NH1" <-> "NH2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D ARG 421": "NH1" <-> "NH2" Residue "D GLU 447": "OE1" <-> "OE2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D ARG 479": "NH1" <-> "NH2" Residue "D ARG 484": "NH1" <-> "NH2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D ARG 498": "NH1" <-> "NH2" Residue "D ARG 508": "NH1" <-> "NH2" Residue "D ARG 556": "NH1" <-> "NH2" Residue "D ARG 560": "NH1" <-> "NH2" Residue "D GLU 567": "OE1" <-> "OE2" Residue "D GLU 570": "OE1" <-> "OE2" Residue "D ARG 580": "NH1" <-> "NH2" Residue "D ARG 583": "NH1" <-> "NH2" Residue "D ARG 585": "NH1" <-> "NH2" Residue "D GLU 592": "OE1" <-> "OE2" Residue "D ARG 617": "NH1" <-> "NH2" Residue "D ARG 634": "NH1" <-> "NH2" Residue "D ARG 650": "NH1" <-> "NH2" Residue "D GLU 658": "OE1" <-> "OE2" Residue "D GLU 661": "OE1" <-> "OE2" Residue "D ARG 666": "NH1" <-> "NH2" Residue "D ARG 668": "NH1" <-> "NH2" Residue "D GLU 669": "OE1" <-> "OE2" Residue "D ARG 679": "NH1" <-> "NH2" Residue "D ARG 691": "NH1" <-> "NH2" Residue "D GLU 695": "OE1" <-> "OE2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "D ARG 722": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 20842 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5154 Classifications: {'peptide': 660} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 623} Chain breaks: 1 Chain: "B" Number of atoms: 5166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5166 Classifications: {'peptide': 662} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 625} Chain breaks: 1 Chain: "C" Number of atoms: 5166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5166 Classifications: {'peptide': 662} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 625} Chain breaks: 1 Chain: "D" Number of atoms: 5166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5166 Classifications: {'peptide': 662} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 625} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 10.85, per 1000 atoms: 0.52 Number of scatterers: 20842 At special positions: 0 Unit cell: (126.36, 98.28, 130.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 44 16.00 O 3947 8.00 N 3589 7.00 C 13258 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 - 3.50 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.36 Conformation dependent library (CDL) restraints added in 3.2 seconds 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4830 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 158 helices and 9 sheets defined 47.5% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.928A pdb=" N LYS A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 83 removed outlier: 4.148A pdb=" N THR A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 97 through 110 removed outlier: 3.637A pdb=" N ARG A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR A 110 " --> pdb=" O HIS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 139 through 156 removed outlier: 3.820A pdb=" N LEU A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TRP A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Proline residue: A 148 - end of helix removed outlier: 6.731A pdb=" N GLN A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LYS A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 172 removed outlier: 4.165A pdb=" N ILE A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 241 through 252 removed outlier: 3.733A pdb=" N MET A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 375 through 382 removed outlier: 4.441A pdb=" N LEU A 380 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 removed outlier: 3.931A pdb=" N LYS A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 413 Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 464 through 475 Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 506 through 519 Proline residue: A 511 - end of helix removed outlier: 3.843A pdb=" N GLU A 514 " --> pdb=" O PRO A 511 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU A 519 " --> pdb=" O ILE A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 543 removed outlier: 3.663A pdb=" N GLY A 533 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 566 through 572 removed outlier: 4.002A pdb=" N LEU A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU A 572 " --> pdb=" O MET A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 580 No H-bonds generated for 'chain 'A' and resid 578 through 580' Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 606 through 618 Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 641 through 647 Processing helix chain 'A' and resid 679 through 685 removed outlier: 5.164A pdb=" N PHE A 684 " --> pdb=" O ALA A 680 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLY A 685 " --> pdb=" O ASP A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 698 removed outlier: 3.662A pdb=" N VAL A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 719 Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 62 through 68 removed outlier: 3.937A pdb=" N LYS B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 83 removed outlier: 4.139A pdb=" N THR B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 97 through 110 removed outlier: 3.523A pdb=" N ARG B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR B 110 " --> pdb=" O HIS B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 139 through 156 removed outlier: 3.806A pdb=" N LEU B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TRP B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Proline residue: B 148 - end of helix removed outlier: 6.722A pdb=" N GLN B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LYS B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 172 removed outlier: 4.158A pdb=" N ILE B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 238 through 252 removed outlier: 3.609A pdb=" N ALA B 242 " --> pdb=" O PRO B 238 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET B 252 " --> pdb=" O THR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 290 through 292 No H-bonds generated for 'chain 'B' and resid 290 through 292' Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 328 through 335 Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 384 through 394 removed outlier: 3.950A pdb=" N LYS B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 413 Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing helix chain 'B' and resid 433 through 435 No H-bonds generated for 'chain 'B' and resid 433 through 435' Processing helix chain 'B' and resid 447 through 458 Processing helix chain 'B' and resid 464 through 475 Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 501 through 503 No H-bonds generated for 'chain 'B' and resid 501 through 503' Processing helix chain 'B' and resid 506 through 519 Proline residue: B 511 - end of helix removed outlier: 3.831A pdb=" N GLU B 514 " --> pdb=" O PRO B 511 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU B 519 " --> pdb=" O ILE B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 543 removed outlier: 3.666A pdb=" N GLY B 533 " --> pdb=" O ILE B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 563 No H-bonds generated for 'chain 'B' and resid 561 through 563' Processing helix chain 'B' and resid 566 through 572 removed outlier: 4.000A pdb=" N LEU B 571 " --> pdb=" O GLU B 567 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU B 572 " --> pdb=" O MET B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 580 No H-bonds generated for 'chain 'B' and resid 578 through 580' Processing helix chain 'B' and resid 591 through 601 Processing helix chain 'B' and resid 606 through 618 Processing helix chain 'B' and resid 623 through 625 No H-bonds generated for 'chain 'B' and resid 623 through 625' Processing helix chain 'B' and resid 641 through 647 Processing helix chain 'B' and resid 679 through 685 removed outlier: 5.147A pdb=" N PHE B 684 " --> pdb=" O ALA B 680 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLY B 685 " --> pdb=" O ASP B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 698 removed outlier: 3.665A pdb=" N VAL B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL B 696 " --> pdb=" O ALA B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 719 Processing helix chain 'C' and resid 43 through 45 No H-bonds generated for 'chain 'C' and resid 43 through 45' Processing helix chain 'C' and resid 62 through 68 removed outlier: 4.011A pdb=" N LYS C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 83 removed outlier: 4.151A pdb=" N THR C 83 " --> pdb=" O LYS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 97 through 110 removed outlier: 3.606A pdb=" N ARG C 102 " --> pdb=" O GLY C 98 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR C 110 " --> pdb=" O HIS C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 126 No H-bonds generated for 'chain 'C' and resid 124 through 126' Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 139 through 156 removed outlier: 3.813A pdb=" N LEU C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TRP C 147 " --> pdb=" O ARG C 143 " (cutoff:3.500A) Proline residue: C 148 - end of helix removed outlier: 6.728A pdb=" N GLN C 155 " --> pdb=" O GLN C 151 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LYS C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 172 removed outlier: 4.148A pdb=" N ILE C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 234 No H-bonds generated for 'chain 'C' and resid 232 through 234' Processing helix chain 'C' and resid 241 through 252 removed outlier: 3.574A pdb=" N MET C 252 " --> pdb=" O THR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 266 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 290 through 292 No H-bonds generated for 'chain 'C' and resid 290 through 292' Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 328 through 335 Processing helix chain 'C' and resid 375 through 377 No H-bonds generated for 'chain 'C' and resid 375 through 377' Processing helix chain 'C' and resid 384 through 394 removed outlier: 3.990A pdb=" N LYS C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE C 389 " --> pdb=" O GLU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 413 Processing helix chain 'C' and resid 419 through 421 No H-bonds generated for 'chain 'C' and resid 419 through 421' Processing helix chain 'C' and resid 433 through 435 No H-bonds generated for 'chain 'C' and resid 433 through 435' Processing helix chain 'C' and resid 447 through 458 Processing helix chain 'C' and resid 464 through 477 removed outlier: 5.122A pdb=" N THR C 477 " --> pdb=" O ALA C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 499 No H-bonds generated for 'chain 'C' and resid 497 through 499' Processing helix chain 'C' and resid 501 through 503 No H-bonds generated for 'chain 'C' and resid 501 through 503' Processing helix chain 'C' and resid 506 through 519 Proline residue: C 511 - end of helix removed outlier: 3.825A pdb=" N GLU C 514 " --> pdb=" O PRO C 511 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU C 519 " --> pdb=" O ILE C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 544 removed outlier: 3.683A pdb=" N GLY C 533 " --> pdb=" O ILE C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 563 No H-bonds generated for 'chain 'C' and resid 561 through 563' Processing helix chain 'C' and resid 566 through 572 removed outlier: 4.062A pdb=" N LEU C 571 " --> pdb=" O GLU C 567 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU C 572 " --> pdb=" O MET C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 580 No H-bonds generated for 'chain 'C' and resid 578 through 580' Processing helix chain 'C' and resid 591 through 601 Processing helix chain 'C' and resid 606 through 618 Processing helix chain 'C' and resid 623 through 625 No H-bonds generated for 'chain 'C' and resid 623 through 625' Processing helix chain 'C' and resid 641 through 647 Processing helix chain 'C' and resid 679 through 685 removed outlier: 5.180A pdb=" N PHE C 684 " --> pdb=" O ALA C 680 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLY C 685 " --> pdb=" O ASP C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 698 removed outlier: 3.661A pdb=" N VAL C 693 " --> pdb=" O VAL C 689 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C 696 " --> pdb=" O ALA C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 719 Processing helix chain 'D' and resid 43 through 45 No H-bonds generated for 'chain 'D' and resid 43 through 45' Processing helix chain 'D' and resid 62 through 68 removed outlier: 3.857A pdb=" N LYS D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 83 removed outlier: 4.164A pdb=" N THR D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 97 through 110 removed outlier: 3.610A pdb=" N ARG D 102 " --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 126 No H-bonds generated for 'chain 'D' and resid 124 through 126' Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 134 through 136 No H-bonds generated for 'chain 'D' and resid 134 through 136' Processing helix chain 'D' and resid 139 through 156 removed outlier: 3.821A pdb=" N LEU D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TRP D 147 " --> pdb=" O ARG D 143 " (cutoff:3.500A) Proline residue: D 148 - end of helix removed outlier: 6.740A pdb=" N GLN D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LYS D 156 " --> pdb=" O LYS D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 172 removed outlier: 4.158A pdb=" N ILE D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 234 No H-bonds generated for 'chain 'D' and resid 232 through 234' Processing helix chain 'D' and resid 240 through 252 removed outlier: 3.591A pdb=" N ALA D 243 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE D 249 " --> pdb=" O ARG D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 266 Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 290 through 292 No H-bonds generated for 'chain 'D' and resid 290 through 292' Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 328 through 334 Processing helix chain 'D' and resid 375 through 381 removed outlier: 4.309A pdb=" N LEU D 380 " --> pdb=" O THR D 376 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG D 381 " --> pdb=" O ASP D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 394 removed outlier: 3.947A pdb=" N LYS D 388 " --> pdb=" O PRO D 384 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE D 389 " --> pdb=" O GLU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 413 Processing helix chain 'D' and resid 419 through 421 No H-bonds generated for 'chain 'D' and resid 419 through 421' Processing helix chain 'D' and resid 433 through 435 No H-bonds generated for 'chain 'D' and resid 433 through 435' Processing helix chain 'D' and resid 447 through 460 Processing helix chain 'D' and resid 464 through 477 removed outlier: 5.143A pdb=" N THR D 477 " --> pdb=" O ALA D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 499 No H-bonds generated for 'chain 'D' and resid 497 through 499' Processing helix chain 'D' and resid 501 through 503 No H-bonds generated for 'chain 'D' and resid 501 through 503' Processing helix chain 'D' and resid 506 through 519 Proline residue: D 511 - end of helix removed outlier: 3.839A pdb=" N GLU D 514 " --> pdb=" O PRO D 511 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU D 519 " --> pdb=" O ILE D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 543 removed outlier: 3.696A pdb=" N GLY D 533 " --> pdb=" O ILE D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 563 No H-bonds generated for 'chain 'D' and resid 561 through 563' Processing helix chain 'D' and resid 566 through 572 removed outlier: 4.157A pdb=" N LEU D 571 " --> pdb=" O GLU D 567 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU D 572 " --> pdb=" O MET D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 580 No H-bonds generated for 'chain 'D' and resid 578 through 580' Processing helix chain 'D' and resid 591 through 601 Processing helix chain 'D' and resid 606 through 618 Processing helix chain 'D' and resid 623 through 625 No H-bonds generated for 'chain 'D' and resid 623 through 625' Processing helix chain 'D' and resid 641 through 647 Processing helix chain 'D' and resid 679 through 685 removed outlier: 5.176A pdb=" N PHE D 684 " --> pdb=" O ALA D 680 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLY D 685 " --> pdb=" O ASP D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 698 removed outlier: 3.663A pdb=" N VAL D 693 " --> pdb=" O VAL D 689 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL D 696 " --> pdb=" O ALA D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 719 Processing sheet with id= A, first strand: chain 'A' and resid 338 through 342 Processing sheet with id= B, first strand: chain 'A' and resid 651 through 655 removed outlier: 3.512A pdb=" N PHE A 675 " --> pdb=" O GLY A 665 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASP A 667 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL A 673 " --> pdb=" O ASP A 667 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 337 through 343 removed outlier: 4.679A pdb=" N GLU B 337 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 651 through 655 removed outlier: 3.538A pdb=" N PHE B 675 " --> pdb=" O GLY B 665 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP B 667 " --> pdb=" O VAL B 673 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL B 673 " --> pdb=" O ASP B 667 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 337 through 342 removed outlier: 4.757A pdb=" N GLU C 337 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 353 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 651 through 655 removed outlier: 7.132A pdb=" N ASP C 667 " --> pdb=" O VAL C 673 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL C 673 " --> pdb=" O ASP C 667 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 359 through 361 removed outlier: 3.629A pdb=" N ASP C 361 " --> pdb=" O LYS C 367 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS C 367 " --> pdb=" O ASP C 361 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 339 through 342 Processing sheet with id= I, first strand: chain 'D' and resid 651 through 655 removed outlier: 3.648A pdb=" N PHE D 675 " --> pdb=" O GLY D 665 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASP D 667 " --> pdb=" O VAL D 673 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL D 673 " --> pdb=" O ASP D 667 " (cutoff:3.500A) 634 hydrogen bonds defined for protein. 1788 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: 6.00 Time building geometry restraints manager: 8.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.33: 4661 1.33 - 1.52: 10007 1.52 - 1.70: 6596 1.70 - 1.89: 88 1.89 - 2.08: 16 Bond restraints: 21368 Sorted by residual: bond pdb=" C VAL C 227 " pdb=" O VAL C 227 " ideal model delta sigma weight residual 1.233 1.138 0.095 1.08e-02 8.57e+03 7.69e+01 bond pdb=" C VAL B 227 " pdb=" O VAL B 227 " ideal model delta sigma weight residual 1.233 1.144 0.089 1.08e-02 8.57e+03 6.78e+01 bond pdb=" C TRP C 89 " pdb=" O TRP C 89 " ideal model delta sigma weight residual 1.238 1.164 0.074 1.28e-02 6.10e+03 3.37e+01 bond pdb=" CA PRO C 90 " pdb=" C PRO C 90 " ideal model delta sigma weight residual 1.521 1.582 -0.061 1.27e-02 6.20e+03 2.32e+01 bond pdb=" C ASN A 280 " pdb=" O ASN A 280 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.29e-02 6.01e+03 2.02e+01 ... (remaining 21363 not shown) Histogram of bond angle deviations from ideal: 88.67 - 106.45: 679 106.45 - 124.24: 27555 124.24 - 142.02: 826 142.02 - 159.80: 0 159.80 - 177.58: 8 Bond angle restraints: 29068 Sorted by residual: angle pdb=" N VAL B 588 " pdb=" CA VAL B 588 " pdb=" C VAL B 588 " ideal model delta sigma weight residual 110.53 126.23 -15.70 9.40e-01 1.13e+00 2.79e+02 angle pdb=" N ILE D 225 " pdb=" CA ILE D 225 " pdb=" C ILE D 225 " ideal model delta sigma weight residual 110.53 123.63 -13.10 9.40e-01 1.13e+00 1.94e+02 angle pdb=" N GLY C 270 " pdb=" CA GLY C 270 " pdb=" C GLY C 270 " ideal model delta sigma weight residual 111.02 127.58 -16.56 1.86e+00 2.89e-01 7.93e+01 angle pdb=" N GLY B 270 " pdb=" CA GLY B 270 " pdb=" C GLY B 270 " ideal model delta sigma weight residual 111.02 127.14 -16.12 1.86e+00 2.89e-01 7.51e+01 angle pdb=" N VAL D 316 " pdb=" CA VAL D 316 " pdb=" C VAL D 316 " ideal model delta sigma weight residual 108.11 119.44 -11.33 1.40e+00 5.10e-01 6.55e+01 ... (remaining 29063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 10623 17.84 - 35.68: 1297 35.68 - 53.52: 447 53.52 - 71.36: 141 71.36 - 89.21: 42 Dihedral angle restraints: 12550 sinusoidal: 5022 harmonic: 7528 Sorted by residual: dihedral pdb=" C VAL B 588 " pdb=" N VAL B 588 " pdb=" CA VAL B 588 " pdb=" CB VAL B 588 " ideal model delta harmonic sigma weight residual -122.00 -136.41 14.41 0 2.50e+00 1.60e-01 3.32e+01 dihedral pdb=" C GLU D 315 " pdb=" N GLU D 315 " pdb=" CA GLU D 315 " pdb=" CB GLU D 315 " ideal model delta harmonic sigma weight residual -122.60 -134.81 12.21 0 2.50e+00 1.60e-01 2.38e+01 dihedral pdb=" CA ASP D 44 " pdb=" C ASP D 44 " pdb=" N LEU D 45 " pdb=" CA LEU D 45 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 12547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.360: 3031 0.360 - 0.719: 12 0.719 - 1.079: 0 1.079 - 1.438: 1 1.438 - 1.798: 7 Chirality restraints: 3051 Sorted by residual: chirality pdb=" CG LEU A 662 " pdb=" CB LEU A 662 " pdb=" CD1 LEU A 662 " pdb=" CD2 LEU A 662 " both_signs ideal model delta sigma weight residual False -2.59 -0.79 -1.80 2.00e-01 2.50e+01 8.08e+01 chirality pdb=" CG LEU B 139 " pdb=" CB LEU B 139 " pdb=" CD1 LEU B 139 " pdb=" CD2 LEU B 139 " both_signs ideal model delta sigma weight residual False -2.59 -0.84 -1.75 2.00e-01 2.50e+01 7.68e+01 chirality pdb=" CG LEU A 193 " pdb=" CB LEU A 193 " pdb=" CD1 LEU A 193 " pdb=" CD2 LEU A 193 " both_signs ideal model delta sigma weight residual False -2.59 -0.84 -1.75 2.00e-01 2.50e+01 7.67e+01 ... (remaining 3048 not shown) Planarity restraints: 3825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP C 89 " 0.064 5.00e-02 4.00e+02 9.70e-02 1.51e+01 pdb=" N PRO C 90 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO C 90 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 90 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 89 " -0.054 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO B 90 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 90 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 90 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 89 " 0.052 5.00e-02 4.00e+02 7.86e-02 9.87e+00 pdb=" N PRO D 90 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 90 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 90 " 0.044 5.00e-02 4.00e+02 ... (remaining 3822 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.96: 8 1.96 - 2.69: 785 2.69 - 3.43: 30095 3.43 - 4.16: 52702 4.16 - 4.90: 91792 Nonbonded interactions: 175382 Sorted by model distance: nonbonded pdb=" CH2 TRP D 105 " pdb=" CE2 TYR D 226 " model vdw 1.219 3.640 nonbonded pdb=" CH2 TRP B 105 " pdb=" CE2 TYR B 226 " model vdw 1.296 3.640 nonbonded pdb=" CH2 TRP C 105 " pdb=" CE2 TYR C 226 " model vdw 1.310 3.640 nonbonded pdb=" CH2 TRP A 105 " pdb=" CE2 TYR A 226 " model vdw 1.357 3.640 nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLN A 324 " model vdw 1.865 2.440 ... (remaining 175377 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 38 through 195 or resid 224 through 725 or resid 1001)) selection = (chain 'C' and (resid 38 through 195 or resid 224 through 725 or resid 1001)) selection = (chain 'D' and (resid 38 through 195 or resid 224 through 725 or resid 1001)) } 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: 0.060 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: 1.870 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 52.340 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.110 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:13.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 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 : 0.009 0.132 21368 Z= 0.571 Angle : 1.038 16.560 29068 Z= 0.598 Chirality : 0.106 1.798 3051 Planarity : 0.007 0.097 3825 Dihedral : 19.126 89.205 7720 Min Nonbonded Distance : 1.219 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 11.17 % Allowed : 17.34 % Favored : 71.48 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 5.56 % 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: -3.03 (0.14), residues: 2630 helix: -1.92 (0.12), residues: 1108 sheet: -0.37 (0.56), residues: 78 loop : -2.21 (0.14), residues: 1444 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 387 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 239 outliers final: 156 residues processed: 585 average time/residue: 1.4618 time to fit residues: 956.0278 Evaluate side-chains 521 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 365 time to evaluate : 2.220 Switching outliers to nearest non-outliers outliers start: 156 outliers final: 136 residues processed: 20 average time/residue: 0.7073 time to fit residues: 20.5696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 239 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN B 125 GLN B 645 ASN C 340 GLN C 628 ASN C 645 ASN D 280 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21368 Z= 0.249 Angle : 0.663 13.167 29068 Z= 0.340 Chirality : 0.044 0.156 3051 Planarity : 0.006 0.059 3825 Dihedral : 6.675 69.587 2886 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 9.07 % Allowed : 20.29 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.27 (0.15), residues: 2630 helix: -0.42 (0.14), residues: 1073 sheet: -0.01 (0.55), residues: 78 loop : -1.19 (0.16), residues: 1479 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 371 time to evaluate : 2.216 Fit side-chains revert: symmetry clash outliers start: 194 outliers final: 128 residues processed: 529 average time/residue: 1.4304 time to fit residues: 847.9286 Evaluate side-chains 485 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 357 time to evaluate : 2.247 Switching outliers to nearest non-outliers outliers start: 128 outliers final: 117 residues processed: 11 average time/residue: 0.3368 time to fit residues: 8.6215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 199 optimal weight: 7.9990 chunk 163 optimal weight: 0.0000 chunk 66 optimal weight: 9.9990 chunk 240 optimal weight: 20.0000 chunk 259 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 192 optimal weight: 0.0470 overall best weight: 2.6088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21368 Z= 0.190 Angle : 0.585 11.896 29068 Z= 0.298 Chirality : 0.042 0.156 3051 Planarity : 0.005 0.051 3825 Dihedral : 6.168 67.400 2886 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 8.13 % Allowed : 21.27 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.53 (0.16), residues: 2630 helix: 0.21 (0.15), residues: 1092 sheet: -0.10 (0.53), residues: 88 loop : -0.77 (0.16), residues: 1450 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 356 time to evaluate : 2.304 Fit side-chains revert: symmetry clash outliers start: 174 outliers final: 123 residues processed: 509 average time/residue: 1.3065 time to fit residues: 743.6314 Evaluate side-chains 478 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 355 time to evaluate : 1.357 Switching outliers to nearest non-outliers outliers start: 123 outliers final: 114 residues processed: 10 average time/residue: 0.3079 time to fit residues: 6.1734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 9.9990 chunk 180 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 241 optimal weight: 8.9990 chunk 255 optimal weight: 7.9990 chunk 125 optimal weight: 0.0970 chunk 228 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 overall best weight: 4.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: