Starting phenix.real_space_refine (version: dev) on Thu Dec 15 13:40:44 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aav_11693/12_2022/7aav_11693_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aav_11693/12_2022/7aav_11693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aav_11693/12_2022/7aav_11693.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aav_11693/12_2022/7aav_11693.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aav_11693/12_2022/7aav_11693_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aav_11693/12_2022/7aav_11693_updated.pdb" } resolution = 4.2 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= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "r ARG 417": "NH1" <-> "NH2" Residue "K ARG 385": "NH1" <-> "NH2" Residue "K ARG 388": "NH1" <-> "NH2" Residue "A ARG 71": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 635": "NH1" <-> "NH2" Residue "A ARG 781": "NH1" <-> "NH2" Residue "A ARG 1100": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 25867 Number of models: 1 Model: "" Number of chains: 19 Chain: "r" Number of atoms: 4834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 895, 4834 Classifications: {'peptide': 895} Incomplete info: {'truncation_to_alanine': 683} Link IDs: {'PTRANS': 55, 'TRANS': 839} Unresolved non-hydrogen bonds: 2309 Unresolved non-hydrogen angles: 2945 Unresolved non-hydrogen dihedrals: 1831 Unresolved non-hydrogen chiralities: 269 Planarities with less than four sites: {'GLN:plan1': 29, 'HIS:plan': 15, 'TYR:plan': 21, 'ASN:plan1': 25, 'TRP:plan': 3, 'ASP:plan': 58, 'PHE:plan': 22, 'GLU:plan': 65, 'ARG:plan': 38} Unresolved non-hydrogen planarities: 1196 Chain: "Q" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 758 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 6, 'TRANS': 131} Unresolved non-hydrogen bonds: 405 Unresolved non-hydrogen angles: 501 Unresolved non-hydrogen dihedrals: 336 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 221 Chain: "L" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 517 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 3, 'TRANS': 99} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 320 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 6, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 211 Chain: "R" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 219 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'TRANS': 43} Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Chain: "K" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 779 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 120} Unresolved non-hydrogen bonds: 282 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 187 Chain: "G" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 1604 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 262} Link IDs: {'PTRANS': 13, 'TRANS': 306} Unresolved non-hydrogen bonds: 968 Unresolved non-hydrogen angles: 1264 Unresolved non-hydrogen dihedrals: 823 Unresolved non-hydrogen chiralities: 98 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 20, 'TYR:plan': 8, 'ASN:plan1': 11, 'TRP:plan': 11, 'HIS:plan': 17, 'PHE:plan': 8, 'GLU:plan': 10, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 551 Chain: "Z" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 622 Classifications: {'RNA': 29} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 13, 'rna3p_pyr': 8} Link IDs: {'rna2p': 8, 'rna3p': 20} Chain: "8" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 92 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 1, 'TRANS': 16} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "I" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 883 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 154} Link IDs: {'PTRANS': 6, 'TRANS': 169} Unresolved non-hydrogen bonds: 601 Unresolved non-hydrogen angles: 764 Unresolved non-hydrogen dihedrals: 500 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 11, 'TYR:plan': 11, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 18, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 347 Chain: "A" Number of atoms: 9649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1656, 9649 Classifications: {'peptide': 1656} Incomplete info: {'truncation_to_alanine': 1171} Link IDs: {'PTRANS': 91, 'TRANS': 1564} Chain breaks: 2 Unresolved non-hydrogen bonds: 4350 Unresolved non-hydrogen angles: 5538 Unresolved non-hydrogen dihedrals: 3563 Unresolved non-hydrogen chiralities: 379 Planarities with less than four sites: {'GLN:plan1': 66, 'ASP:plan': 98, 'TYR:plan': 40, 'ASN:plan1': 83, 'TRP:plan': 17, 'HIS:plan': 38, 'PHE:plan': 43, 'GLU:plan': 92, 'ARG:plan': 103} Unresolved non-hydrogen planarities: 2571 Chain: "P" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 825 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 134} Link IDs: {'PTRANS': 12, 'TRANS': 149} Chain breaks: 1 Unresolved non-hydrogen bonds: 519 Unresolved non-hydrogen angles: 655 Unresolved non-hydrogen dihedrals: 442 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 3, 'ASP:plan': 12, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 299 Chain: "v" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1053 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PTRANS': 15, 'TRANS': 190} Chain breaks: 3 Unresolved non-hydrogen bonds: 645 Unresolved non-hydrogen angles: 799 Unresolved non-hydrogen dihedrals: 546 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 9, 'PHE:plan': 5, 'GLU:plan': 22, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 395 Chain: "N" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 277 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'TRANS': 55} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 103 Chain: "2" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 215 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "5" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1453 Classifications: {'RNA': 69} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 5, 'rna3p_pur': 19, 'rna3p_pyr': 34} Link IDs: {'rna2p': 16, 'rna3p': 52} Chain: "6" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1560 Classifications: {'RNA': 73} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 7, 'rna3p_pur': 33, 'rna3p_pyr': 25} Link IDs: {'rna2p': 15, 'rna3p': 57} Chain breaks: 1 Chain: "q" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 458 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'TRANS': 72} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 73 Chain: "r" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'KGN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.99, per 1000 atoms: 0.62 Number of scatterers: 25867 At special positions: 0 Unit cell: (190.24, 156.6, 171.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 7 16.00 P 190 15.00 Mg 1 11.99 O 5347 8.00 N 4868 7.00 C 15454 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.98 Conformation dependent library (CDL) restraints added in 4.7 seconds 7864 Ramachandran restraints generated. 3932 Oldfield, 0 Emsley, 3932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7550 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 25 sheets defined 33.8% alpha, 6.3% beta 41 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 9.69 Creating SS restraints... Processing helix chain 'r' and resid 119 through 124 removed outlier: 3.552A pdb=" N MET r 123 " --> pdb=" O LEU r 119 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP r 124 " --> pdb=" O ALA r 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 119 through 124' Processing helix chain 'r' and resid 143 through 153 removed outlier: 3.643A pdb=" N ASP r 147 " --> pdb=" O THR r 143 " (cutoff:3.500A) Processing helix chain 'r' and resid 172 through 177 Processing helix chain 'r' and resid 209 through 219 removed outlier: 3.867A pdb=" N SER r 212 " --> pdb=" O VAL r 209 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASP r 213 " --> pdb=" O ASN r 210 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR r 216 " --> pdb=" O ASP r 213 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA r 217 " --> pdb=" O GLU r 214 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU r 219 " --> pdb=" O THR r 216 " (cutoff:3.500A) Processing helix chain 'r' and resid 237 through 248 Processing helix chain 'r' and resid 260 through 265 removed outlier: 4.366A pdb=" N LEU r 265 " --> pdb=" O ARG r 262 " (cutoff:3.500A) Processing helix chain 'r' and resid 271 through 289 removed outlier: 3.544A pdb=" N TYR r 275 " --> pdb=" O PRO r 271 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR r 276 " --> pdb=" O THR r 272 " (cutoff:3.500A) Processing helix chain 'r' and resid 320 through 329 removed outlier: 3.641A pdb=" N ALA r 324 " --> pdb=" O LEU r 320 " (cutoff:3.500A) Processing helix chain 'r' and resid 369 through 372 No H-bonds generated for 'chain 'r' and resid 369 through 372' Processing helix chain 'r' and resid 374 through 385 removed outlier: 3.560A pdb=" N VAL r 384 " --> pdb=" O ILE r 380 " (cutoff:3.500A) Processing helix chain 'r' and resid 392 through 398 Processing helix chain 'r' and resid 405 through 408 No H-bonds generated for 'chain 'r' and resid 405 through 408' Processing helix chain 'r' and resid 412 through 423 Processing helix chain 'r' and resid 428 through 435 Processing helix chain 'r' and resid 446 through 452 Processing helix chain 'r' and resid 461 through 464 No H-bonds generated for 'chain 'r' and resid 461 through 464' Processing helix chain 'r' and resid 600 through 613 Processing helix chain 'r' and resid 634 through 646 removed outlier: 3.584A pdb=" N ASP r 643 " --> pdb=" O CYS r 639 " (cutoff:3.500A) Processing helix chain 'r' and resid 694 through 701 Processing helix chain 'r' and resid 711 through 720 removed outlier: 3.514A pdb=" N PHE r 717 " --> pdb=" O LYS r 713 " (cutoff:3.500A) Processing helix chain 'r' and resid 726 through 730 Processing helix chain 'r' and resid 737 through 739 No H-bonds generated for 'chain 'r' and resid 737 through 739' Processing helix chain 'r' and resid 765 through 773 Processing helix chain 'r' and resid 807 through 821 Processing helix chain 'r' and resid 844 through 852 Processing helix chain 'r' and resid 883 through 890 Processing helix chain 'r' and resid 929 through 939 removed outlier: 3.521A pdb=" N ARG r 938 " --> pdb=" O MET r 934 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ARG r 939 " --> pdb=" O ILE r 935 " (cutoff:3.500A) Processing helix chain 'r' and resid 949 through 952 Processing helix chain 'Q' and resid 19 through 33 Processing helix chain 'Q' and resid 47 through 64 removed outlier: 3.682A pdb=" N ILE Q 60 " --> pdb=" O LYS Q 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 72 through 81 Processing helix chain 'Q' and resid 86 through 93 Processing helix chain 'L' and resid 13 through 24 Processing helix chain 'L' and resid 31 through 38 removed outlier: 3.706A pdb=" N LEU L 37 " --> pdb=" O ARG L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 49 Processing helix chain 'L' and resid 65 through 77 removed outlier: 3.708A pdb=" N LYS L 76 " --> pdb=" O LEU L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 89 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 96 through 107 Processing helix chain 'R' and resid 218 through 223 Processing helix chain 'K' and resid 272 through 313 removed outlier: 3.864A pdb=" N LEU K 297 " --> pdb=" O ASP K 293 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU K 298 " --> pdb=" O ARG K 294 " (cutoff:3.500A) Processing helix chain '8' and resid 122 through 130 removed outlier: 3.506A pdb=" N ARG 8 130 " --> pdb=" O GLU 8 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 30 removed outlier: 3.748A pdb=" N ARG I 28 " --> pdb=" O ILE I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 36 No H-bonds generated for 'chain 'I' and resid 33 through 36' Processing helix chain 'I' and resid 44 through 53 removed outlier: 3.657A pdb=" N VAL I 48 " --> pdb=" O ALA I 44 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU I 53 " --> pdb=" O ASP I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 80 Processing helix chain 'I' and resid 84 through 92 Processing helix chain 'I' and resid 97 through 110 removed outlier: 3.664A pdb=" N TYR I 106 " --> pdb=" O LEU I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 120 Processing helix chain 'I' and resid 122 through 125 removed outlier: 3.541A pdb=" N ASN I 125 " --> pdb=" O PRO I 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 122 through 125' Processing helix chain 'I' and resid 144 through 151 Processing helix chain 'I' and resid 168 through 174 removed outlier: 3.540A pdb=" N GLU I 173 " --> pdb=" O TYR I 169 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA I 174 " --> pdb=" O VAL I 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 85 through 93 removed outlier: 3.846A pdb=" N LEU A 92 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 137 through 157 removed outlier: 3.516A pdb=" N LYS A 155 " --> pdb=" O MET A 151 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 214 No H-bonds generated for 'chain 'A' and resid 211 through 214' Processing helix chain 'A' and resid 232 through 244 removed outlier: 3.686A pdb=" N ARG A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 268 Processing helix chain 'A' and resid 310 through 315 removed outlier: 3.522A pdb=" N ALA A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 320 No H-bonds generated for 'chain 'A' and resid 317 through 320' Processing helix chain 'A' and resid 372 through 379 removed outlier: 4.532A pdb=" N GLU A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 405 removed outlier: 3.625A pdb=" N ALA A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 441 through 459 removed outlier: 4.240A pdb=" N VAL A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 458 " --> pdb=" O TYR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 477 No H-bonds generated for 'chain 'A' and resid 474 through 477' Processing helix chain 'A' and resid 489 through 511 removed outlier: 3.500A pdb=" N VAL A 496 " --> pdb=" O VAL A 492 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 538 No H-bonds generated for 'chain 'A' and resid 535 through 538' Processing helix chain 'A' and resid 544 through 566 removed outlier: 3.545A pdb=" N LEU A 551 " --> pdb=" O CYS A 547 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N HIS A 561 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 566 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 587 removed outlier: 3.870A pdb=" N VAL A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLY A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 616 removed outlier: 3.732A pdb=" N TYR A 614 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 651 removed outlier: 3.780A pdb=" N TRP A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) Proline residue: A 646 - end of helix removed outlier: 4.065A pdb=" N GLU A 649 " --> pdb=" O THR A 645 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG A 650 " --> pdb=" O PRO A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 693 Processing helix chain 'A' and resid 707 through 721 Processing helix chain 'A' and resid 733 through 759 Processing helix chain 'A' and resid 771 through 796 Processing helix chain 'A' and resid 803 through 820 removed outlier: 4.093A pdb=" N ALA A 808 " --> pdb=" O GLU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 850 Processing helix chain 'A' and resid 858 through 871 removed outlier: 4.308A pdb=" N GLU A 862 " --> pdb=" O GLN A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 886 Processing helix chain 'A' and resid 913 through 933 removed outlier: 3.754A pdb=" N ILE A 917 " --> pdb=" O PRO A 913 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 922 " --> pdb=" O THR A 918 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS A 932 " --> pdb=" O TYR A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 960 removed outlier: 3.861A pdb=" N LYS A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP A 955 " --> pdb=" O LEU A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1000 Processing helix chain 'A' and resid 1003 through 1012 removed outlier: 3.536A pdb=" N TYR A1008 " --> pdb=" O ASN A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1052 removed outlier: 4.424A pdb=" N SER A1038 " --> pdb=" O GLN A1035 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE A1039 " --> pdb=" O PHE A1036 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A1040 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN A1042 " --> pdb=" O PHE A1039 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A1044 " --> pdb=" O VAL A1041 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A1046 " --> pdb=" O TYR A1043 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET A1048 " --> pdb=" O GLY A1045 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP A1049 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A1050 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A1052 " --> pdb=" O ASP A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1061 Processing helix chain 'A' and resid 1077 through 1081 Processing helix chain 'A' and resid 1103 through 1116 Processing helix chain 'A' and resid 1123 through 1125 No H-bonds generated for 'chain 'A' and resid 1123 through 1125' Processing helix chain 'A' and resid 1144 through 1160 removed outlier: 3.676A pdb=" N PHE A1154 " --> pdb=" O GLY A1150 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A1157 " --> pdb=" O VAL A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1201 No H-bonds generated for 'chain 'A' and resid 1199 through 1201' Processing helix chain 'A' and resid 1234 through 1249 Processing helix chain 'A' and resid 1256 through 1273 removed outlier: 3.504A pdb=" N TRP A1263 " --> pdb=" O ILE A1259 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR A1273 " --> pdb=" O GLY A1269 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1303 removed outlier: 3.504A pdb=" N ASN A1293 " --> pdb=" O VAL A1289 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY A1302 " --> pdb=" O ARG A1298 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A1303 " --> pdb=" O ILE A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1317 removed outlier: 4.179A pdb=" N TYR A1317 " --> pdb=" O VAL A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1339 No H-bonds generated for 'chain 'A' and resid 1337 through 1339' Processing helix chain 'A' and resid 1375 through 1398 removed outlier: 3.678A pdb=" N ARG A1384 " --> pdb=" O ILE A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1419 through 1422 No H-bonds generated for 'chain 'A' and resid 1419 through 1422' Processing helix chain 'A' and resid 1427 through 1432 removed outlier: 3.534A pdb=" N ALA A1431 " --> pdb=" O ARG A1427 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR A1432 " --> pdb=" O HIS A1428 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1427 through 1432' Processing helix chain 'A' and resid 1436 through 1446 removed outlier: 3.548A pdb=" N PHE A1442 " --> pdb=" O VAL A1438 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A1444 " --> pdb=" O THR A1440 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR A1445 " --> pdb=" O ASP A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1478 removed outlier: 4.039A pdb=" N THR A1472 " --> pdb=" O ASN A1468 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A1473 " --> pdb=" O ASN A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1486 Processing helix chain 'A' and resid 1490 through 1493 No H-bonds generated for 'chain 'A' and resid 1490 through 1493' Processing helix chain 'A' and resid 1529 through 1537 Processing helix chain 'A' and resid 1539 through 1542 No H-bonds generated for 'chain 'A' and resid 1539 through 1542' Processing helix chain 'A' and resid 1567 through 1576 removed outlier: 4.134A pdb=" N ILE A1571 " --> pdb=" O PRO A1567 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A1572 " --> pdb=" O THR A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1582 through 1599 Processing helix chain 'A' and resid 1671 through 1673 No H-bonds generated for 'chain 'A' and resid 1671 through 1673' Processing helix chain 'A' and resid 1676 through 1686 removed outlier: 3.610A pdb=" N ARG A1681 " --> pdb=" O GLU A1677 " (cutoff:3.500A) Processing helix chain 'A' and resid 1723 through 1734 removed outlier: 3.725A pdb=" N LYS A1732 " --> pdb=" O GLN A1728 " (cutoff:3.500A) Processing helix chain 'A' and resid 1738 through 1751 removed outlier: 3.733A pdb=" N VAL A1742 " --> pdb=" O PRO A1738 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 97 No H-bonds generated for 'chain 'P' and resid 94 through 97' Processing helix chain 'P' and resid 146 through 150 Processing helix chain 'P' and resid 166 through 169 No H-bonds generated for 'chain 'P' and resid 166 through 169' Processing helix chain 'P' and resid 176 through 178 No H-bonds generated for 'chain 'P' and resid 176 through 178' Processing helix chain 'P' and resid 192 through 194 No H-bonds generated for 'chain 'P' and resid 192 through 194' Processing helix chain 'P' and resid 198 through 202 Processing helix chain 'P' and resid 208 through 215 Processing helix chain 'v' and resid 137 through 161 Processing helix chain 'v' and resid 239 through 244 removed outlier: 4.092A pdb=" N GLN v 242 " --> pdb=" O VAL v 239 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU v 244 " --> pdb=" O GLU v 241 " (cutoff:3.500A) Processing helix chain 'v' and resid 282 through 325 removed outlier: 3.518A pdb=" N GLU v 300 " --> pdb=" O ARG v 296 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 99 removed outlier: 3.568A pdb=" N ILE N 99 " --> pdb=" O PHE N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 133 Processing helix chain 'q' and resid 24 through 35 removed outlier: 3.543A pdb=" N LYS q 29 " --> pdb=" O GLY q 25 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN q 34 " --> pdb=" O LEU q 30 " (cutoff:3.500A) Processing helix chain 'q' and resid 39 through 41 No H-bonds generated for 'chain 'q' and resid 39 through 41' Processing sheet with id= A, first strand: chain 'r' and resid 184 through 187 Processing sheet with id= B, first strand: chain 'r' and resid 226 through 230 removed outlier: 6.297A pdb=" N THR r 254 " --> pdb=" O LEU r 227 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE r 229 " --> pdb=" O THR r 254 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N CYS r 256 " --> pdb=" O ILE r 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'r' and resid 476 through 478 Processing sheet with id= D, first strand: chain 'r' and resid 588 through 591 Processing sheet with id= E, first strand: chain 'r' and resid 592 through 594 Processing sheet with id= F, first strand: chain 'r' and resid 899 through 902 removed outlier: 4.200A pdb=" N TYR r 831 " --> pdb=" O HIS r 902 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE r 874 " --> pdb=" O VAL r 857 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N VAL r 857 " --> pdb=" O PHE r 874 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'r' and resid 686 through 690 removed outlier: 3.741A pdb=" N ASP r 793 " --> pdb=" O THR r 686 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE r 688 " --> pdb=" O ILE r 791 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ILE r 791 " --> pdb=" O ILE r 688 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU r 690 " --> pdb=" O PHE r 789 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE r 789 " --> pdb=" O GLU r 690 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 210 through 212 removed outlier: 5.464A pdb=" N ASP G 232 " --> pdb=" O LEU G 238 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU G 238 " --> pdb=" O ASP G 232 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 313 through 316 Processing sheet with id= J, first strand: chain 'G' and resid 355 through 358 Processing sheet with id= K, first strand: chain 'G' and resid 437 through 440 Processing sheet with id= L, first strand: chain 'G' and resid 194 through 200 removed outlier: 7.113A pdb=" N VAL G 488 " --> pdb=" O TYR G 197 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N VAL G 199 " --> pdb=" O ILE G 486 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILE G 486 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 249 through 254 removed outlier: 6.352A pdb=" N CYS G 264 " --> pdb=" O ARG G 250 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL G 252 " --> pdb=" O PHE G 262 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N PHE G 262 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 129 through 133 Processing sheet with id= O, first strand: chain 'A' and resid 115 through 120 Processing sheet with id= P, first strand: chain 'A' and resid 516 through 518 Processing sheet with id= Q, first strand: chain 'A' and resid 895 through 898 Processing sheet with id= R, first strand: chain 'A' and resid 1174 through 1178 Processing sheet with id= S, first strand: chain 'A' and resid 1185 through 1188 removed outlier: 3.511A pdb=" N THR A1225 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU A1216 " --> pdb=" O THR A1225 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLN A1227 " --> pdb=" O TRP A1214 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP A1214 " --> pdb=" O GLN A1227 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 1341 through 1345 removed outlier: 3.698A pdb=" N LYS A1344 " --> pdb=" O THR A1351 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 1642 through 1644 Processing sheet with id= V, first strand: chain 'A' and resid 1665 through 1667 removed outlier: 3.984A pdb=" N ILE A1705 " --> pdb=" O GLN A1665 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'P' and resid 36 through 39 Processing sheet with id= X, first strand: chain 'q' and resid 2 through 7 Processing sheet with id= Y, first strand: chain 'q' and resid 42 through 45 896 hydrogen bonds defined for protein. 2577 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 166 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 11.37 Time building geometry restraints manager: 11.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6450 1.33 - 1.45: 5655 1.45 - 1.57: 14241 1.57 - 1.69: 368 1.69 - 1.81: 13 Bond restraints: 26727 Sorted by residual: bond pdb=" C CYS A 435 " pdb=" N PRO A 436 " ideal model delta sigma weight residual 1.333 1.380 -0.046 1.01e-02 9.80e+03 2.10e+01 bond pdb=" N ILE A1416 " pdb=" CA ILE A1416 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.23e-02 6.61e+03 6.85e+00 bond pdb=" N ARG A1418 " pdb=" CA ARG A1418 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.28e-02 6.10e+03 6.50e+00 bond pdb=" N ASP A1413 " pdb=" CA ASP A1413 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.49e+00 bond pdb=" N ARG A1414 " pdb=" CA ARG A1414 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.34e+00 ... (remaining 26722 not shown) Histogram of bond angle deviations from ideal: 100.02 - 107.14: 2024 107.14 - 114.26: 15078 114.26 - 121.37: 12980 121.37 - 128.49: 7503 128.49 - 135.61: 379 Bond angle restraints: 37964 Sorted by residual: angle pdb=" C TYR A 219 " pdb=" N VAL A 220 " pdb=" CA VAL A 220 " ideal model delta sigma weight residual 120.69 128.25 -7.56 1.46e+00 4.69e-01 2.68e+01 angle pdb=" C3' A 5 26 " pdb=" O3' A 5 26 " pdb=" P U 5 27 " ideal model delta sigma weight residual 120.20 127.55 -7.35 1.50e+00 4.44e-01 2.40e+01 angle pdb=" C3' G 6 49 " pdb=" O3' G 6 49 " pdb=" P A 6 50 " ideal model delta sigma weight residual 120.20 127.24 -7.04 1.50e+00 4.44e-01 2.20e+01 angle pdb=" C THR A 802 " pdb=" N ALA A 803 " pdb=" CA ALA A 803 " ideal model delta sigma weight residual 120.38 127.03 -6.65 1.46e+00 4.69e-01 2.07e+01 angle pdb=" C GLY P 42 " pdb=" N LYS P 43 " pdb=" CA LYS P 43 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.00e+01 ... (remaining 37959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 14994 35.50 - 71.00: 179 71.00 - 106.50: 20 106.50 - 142.00: 1 142.00 - 177.50: 9 Dihedral angle restraints: 15203 sinusoidal: 3646 harmonic: 11557 Sorted by residual: dihedral pdb=" O4' C 6 60 " pdb=" C1' C 6 60 " pdb=" N1 C 6 60 " pdb=" C2 C 6 60 " ideal model delta sinusoidal sigma weight residual 200.00 44.08 155.92 1 1.50e+01 4.44e-03 8.16e+01 dihedral pdb=" O4' C 5 68 " pdb=" C1' C 5 68 " pdb=" N1 C 5 68 " pdb=" C2 C 5 68 " ideal model delta sinusoidal sigma weight residual 200.00 46.01 153.99 1 1.50e+01 4.44e-03 8.10e+01 dihedral pdb=" O4' C 6 37 " pdb=" C1' C 6 37 " pdb=" N1 C 6 37 " pdb=" C2 C 6 37 " ideal model delta sinusoidal sigma weight residual -128.00 49.50 -177.50 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 15200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.029: 4796 1.029 - 2.058: 0 2.058 - 3.087: 0 3.087 - 4.116: 0 4.116 - 5.145: 4 Chirality restraints: 4800 Sorted by residual: chirality pdb=" C1 KGN A3001 " pdb=" C2 KGN A3001 " pdb=" C6 KGN A3001 " pdb=" O11 KGN A3001 " both_signs ideal model delta sigma weight residual False 2.53 -2.61 5.14 2.00e-01 2.50e+01 6.62e+02 chirality pdb=" C3 KGN A3001 " pdb=" C2 KGN A3001 " pdb=" C4 KGN A3001 " pdb=" O13 KGN A3001 " both_signs ideal model delta sigma weight residual False 2.49 -2.54 5.03 2.00e-01 2.50e+01 6.32e+02 chirality pdb=" C5 KGN A3001 " pdb=" C4 KGN A3001 " pdb=" C6 KGN A3001 " pdb=" O15 KGN A3001 " both_signs ideal model delta sigma weight residual False 2.36 -2.50 4.86 2.00e-01 2.50e+01 5.90e+02 ... (remaining 4797 not shown) Planarity restraints: 4561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO v 222 " 0.051 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO v 223 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO v 223 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO v 223 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 947 " 0.050 5.00e-02 4.00e+02 7.41e-02 8.78e+00 pdb=" N PRO A 948 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 948 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 948 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 946 " 0.043 5.00e-02 4.00e+02 6.53e-02 6.83e+00 pdb=" N PRO A 947 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 947 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 947 " 0.036 5.00e-02 4.00e+02 ... (remaining 4558 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 477 2.67 - 3.23: 22618 3.23 - 3.79: 38469 3.79 - 4.34: 43756 4.34 - 4.90: 69930 Nonbonded interactions: 175250 Sorted by model distance: nonbonded pdb=" O1G GTP r1500 " pdb="MG MG r1501 " model vdw 2.116 2.170 nonbonded pdb=" O3A GTP r1500 " pdb="MG MG r1501 " model vdw 2.148 2.170 nonbonded pdb=" O2B GTP r1500 " pdb="MG MG r1501 " model vdw 2.236 2.170 nonbonded pdb=" O GLY A 586 " pdb=" OH TYR A 592 " model vdw 2.286 2.440 nonbonded pdb=" O SER r 183 " pdb=" OH TYR r 482 " model vdw 2.312 2.440 ... (remaining 175245 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 190 5.49 5 Mg 1 5.21 5 S 7 5.16 5 C 15454 2.51 5 N 4868 2.21 5 O 5347 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 3.220 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: 0.020 Extract box with map and model: 14.560 Check model and map are aligned: 0.400 Convert atoms to be neutral: 0.210 Process input model: 74.840 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 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 : 0.003 0.061 26727 Z= 0.214 Angle : 0.781 13.055 37964 Z= 0.439 Chirality : 0.148 5.145 4800 Planarity : 0.006 0.077 4561 Dihedral : 12.592 177.497 7653 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.88 % Favored : 91.07 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -6.29 (0.09), residues: 3932 helix: -4.97 (0.03), residues: 1467 sheet: -3.00 (0.26), residues: 330 loop : -3.87 (0.11), residues: 2135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7864 Ramachandran restraints generated. 3932 Oldfield, 0 Emsley, 3932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7864 Ramachandran restraints generated. 3932 Oldfield, 0 Emsley, 3932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 2.793 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.3484 time to fit residues: 134.7919 Evaluate side-chains 169 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 2.753 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 343 optimal weight: 0.7980 chunk 308 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 208 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 319 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 369 optimal weight: 20.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** r 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 HIS A 545 HIS ** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 26727 Z= 0.385 Angle : 0.759 10.851 37964 Z= 0.406 Chirality : 0.047 0.517 4800 Planarity : 0.006 0.070 4561 Dihedral : 13.595 175.579 6210 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 13.20 % Favored : 86.78 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -4.13 (0.11), residues: 3932 helix: -2.06 (0.11), residues: 1457 sheet: -2.74 (0.25), residues: 365 loop : -3.34 (0.12), residues: 2110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7864 Ramachandran restraints generated. 3932 Oldfield, 0 Emsley, 3932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7864 Ramachandran restraints generated. 3932 Oldfield, 0 Emsley, 3932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 2.734 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.2823 time to fit residues: 83.6144 Evaluate side-chains 143 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 2.918 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 205 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 307 optimal weight: 7.9990 chunk 251 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 370 optimal weight: 9.9990 chunk 399 optimal weight: 5.9990 chunk 329 optimal weight: 4.9990 chunk 367 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** r 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 GLN A 601 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 26727 Z= 0.364 Angle : 0.721 9.160 37964 Z= 0.385 Chirality : 0.046 0.289 4800 Planarity : 0.006 0.071 4561 Dihedral : 14.004 179.952 6210 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.89 % Favored : 86.06 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.96 (0.13), residues: 3932 helix: -0.36 (0.13), residues: 1451 sheet: -2.64 (0.24), residues: 378 loop : -3.15 (0.13), residues: 2103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7864 Ramachandran restraints generated. 3932 Oldfield, 0 Emsley, 3932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7864 Ramachandran restraints generated. 3932 Oldfield, 0 Emsley, 3932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 3.037 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.3045 time to fit residues: 83.3526 Evaluate side-chains 132 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 2.935 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 365 optimal weight: 10.0000 chunk 278 optimal weight: 3.9990 chunk 192 optimal weight: 0.0060 chunk 40 optimal weight: 10.0000 chunk 176 optimal weight: 0.7980 chunk 248 optimal weight: 8.9990 chunk 371 optimal weight: 0.0980 chunk 393 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 352 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** r 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 26727 Z= 0.254 Angle : 0.617 8.662 37964 Z= 0.323 Chirality : 0.044 0.240 4800 Planarity : 0.005 0.062 4561 Dihedral : 13.812 177.420 6210 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.48 % Favored : 86.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.35 (0.14), residues: 3932 helix: 0.43 (0.14), residues: 1460 sheet: -2.45 (0.25), residues: 381 loop : -3.00 (0.13), residues: 2091 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7864 Ramachandran restraints generated. 3932 Oldfield, 0 Emsley, 3932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7864 Ramachandran restraints generated. 3932 Oldfield, 0 Emsley, 3932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 2.738 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2879 time to fit residues: 79.1756 Evaluate side-chains 136 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 3.044 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 327 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 292 optimal weight: 0.9990 chunk 162 optimal weight: 20.0000 chunk 335 optimal weight: 10.0000 chunk 271 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 200 optimal weight: 4.9990 chunk 353 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: r 903 HIS A 579 GLN A1563 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 26727 Z= 0.371 Angle : 0.719 9.417 37964 Z= 0.384 Chirality : 0.047 0.279 4800 Planarity : 0.005 0.069 4561 Dihedral : 14.135 178.318 6210 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 16.38 % Favored : 83.60 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.36 (0.14), residues: 3932 helix: 0.47 (0.14), residues: 1424 sheet: -2.40 (0.25), residues: 385 loop : -3.00 (0.13), residues: 2123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7864 Ramachandran restraints generated. 3932 Oldfield, 0 Emsley, 3932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7864 Ramachandran restraints generated. 3932 Oldfield, 0 Emsley, 3932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 2.979 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.3372 time to fit residues: 91.9293 Evaluate side-chains 131 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 6.179 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 132 optimal weight: 10.0000 chunk 354 optimal weight: 0.0270 chunk 77 optimal weight: 3.9990 chunk 230 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 393 optimal weight: 10.0000 chunk 326 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 206 optimal weight: 3.9990 overall best weight: 2.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 26727 Z= 0.295 Angle : 0.651 9.073 37964 Z= 0.343 Chirality : 0.045 0.254 4800 Planarity : 0.005 0.069 4561 Dihedral : 14.055 179.564 6210 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.75 % Favored : 85.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.18 (0.14), residues: 3932 helix: 0.73 (0.15), residues: 1424 sheet: -2.38 (0.25), residues: 393 loop : -2.97 (0.13), residues: 2115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7864 Ramachandran restraints generated. 3932 Oldfield, 0 Emsley, 3932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7864 Ramachandran restraints generated. 3932 Oldfield, 0 Emsley, 3932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 2.749 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2938 time to fit residues: 84.8255 Evaluate side-chains 139 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 2.543 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 379 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 224 optimal weight: 0.4980 chunk 287 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 chunk 331 optimal weight: 0.0970 chunk 219 optimal weight: 2.9990 chunk 392 optimal weight: 5.9990 chunk 245 optimal weight: 0.0470 chunk 239 optimal weight: 2.9990 chunk 181 optimal weight: 9.9990 overall best weight: 1.3280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 105 ASN ** A1026 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 26727 Z= 0.184 Angle : 0.577 8.859 37964 Z= 0.297 Chirality : 0.043 0.218 4800 Planarity : 0.004 0.059 4561 Dihedral : 13.753 179.713 6210 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.77 % Favored : 87.23 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.70 (0.14), residues: 3932 helix: 1.27 (0.15), residues: 1425 sheet: -2.24 (0.25), residues: 391 loop : -2.78 (0.14), residues: 2116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7864 Ramachandran restraints generated. 3932 Oldfield, 0 Emsley, 3932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7864 Ramachandran restraints generated. 3932 Oldfield, 0 Emsley, 3932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.784 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2853 time to fit residues: 82.1697 Evaluate side-chains 140 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.710 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 242 optimal weight: 0.0470 chunk 156 optimal weight: 20.0000 chunk 234 optimal weight: 4.9990 chunk 118 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 249 optimal weight: 0.0870 chunk 267 optimal weight: 0.0570 chunk 193 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 308 optimal weight: 8.9990 overall best weight: 1.0378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 GLN ** A1026 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1674 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 26727 Z= 0.162 Angle : 0.558 9.166 37964 Z= 0.285 Chirality : 0.042 0.222 4800 Planarity : 0.004 0.056 4561 Dihedral : 13.568 179.900 6210 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.44 (0.15), residues: 3932 helix: 1.58 (0.15), residues: 1424 sheet: -2.13 (0.25), residues: 389 loop : -2.69 (0.14), residues: 2119 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7864 Ramachandran restraints generated. 3932 Oldfield, 0 Emsley, 3932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7864 Ramachandran restraints generated. 3932 Oldfield, 0 Emsley, 3932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.754 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2938 time to fit residues: 86.8422 Evaluate side-chains 139 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 3.030 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 356 optimal weight: 9.9990 chunk 375 optimal weight: 0.8980 chunk 342 optimal weight: 0.0370 chunk 365 optimal weight: 1.9990 chunk 220 optimal weight: 0.0040 chunk 159 optimal weight: 20.0000 chunk 287 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 330 optimal weight: 10.0000 chunk 345 optimal weight: 9.9990 chunk 364 optimal weight: 6.9990 overall best weight: 1.7874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 GLN ** A1026 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 26727 Z= 0.223 Angle : 0.588 9.015 37964 Z= 0.303 Chirality : 0.043 0.232 4800 Planarity : 0.004 0.058 4561 Dihedral : 13.618 178.913 6210 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.50 % Favored : 86.50 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.45 (0.14), residues: 3932 helix: 1.54 (0.15), residues: 1424 sheet: -2.09 (0.25), residues: 391 loop : -2.68 (0.14), residues: 2117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7864 Ramachandran restraints generated. 3932 Oldfield, 0 Emsley, 3932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7864 Ramachandran restraints generated. 3932 Oldfield, 0 Emsley, 3932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.908 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2978 time to fit residues: 84.4257 Evaluate side-chains 143 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 2.905 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 240 optimal weight: 6.9990 chunk 386 optimal weight: 9.9990 chunk 235 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 268 optimal weight: 0.8980 chunk 405 optimal weight: 3.9990 chunk 373 optimal weight: 6.9990 chunk 322 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 249 optimal weight: 0.7980 chunk 197 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1026 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 26727 Z= 0.149 Angle : 0.551 8.076 37964 Z= 0.279 Chirality : 0.042 0.228 4800 Planarity : 0.004 0.054 4561 Dihedral : 13.483 179.769 6210 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.24 (0.15), residues: 3932 helix: 1.74 (0.15), residues: 1434 sheet: -2.00 (0.25), residues: 393 loop : -2.59 (0.14), residues: 2105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7864 Ramachandran restraints generated. 3932 Oldfield, 0 Emsley, 3932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7864 Ramachandran restraints generated. 3932 Oldfield, 0 Emsley, 3932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 2.723 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2937 time to fit residues: 86.3520 Evaluate side-chains 143 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 2.834 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 256 optimal weight: 5.9990 chunk 343 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 297 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 323 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 332 optimal weight: 7.9990 chunk 40 optimal weight: 0.0980 chunk 59 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 GLN ** A1026 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.091991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.077469 restraints weight = 115817.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.077553 restraints weight = 131776.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.077819 restraints weight = 112339.481| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 26727 Z= 0.227 Angle : 0.585 9.529 37964 Z= 0.300 Chirality : 0.043 0.237 4800 Planarity : 0.004 0.058 4561 Dihedral : 13.547 178.903 6210 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.89 % Favored : 86.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.30 (0.15), residues: 3932 helix: 1.70 (0.15), residues: 1421 sheet: -1.95 (0.26), residues: 391 loop : -2.63 (0.14), residues: 2120 =============================================================================== Job complete usr+sys time: 3513.78 seconds wall clock time: 64 minutes 41.91 seconds (3881.91 seconds total)