Starting phenix.real_space_refine on Thu Mar 5 23:27:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aav_11693/03_2026/7aav_11693.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aav_11693/03_2026/7aav_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 { model { file = "/net/cci-nas-00/data/ceres_data/7aav_11693/03_2026/7aav_11693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aav_11693/03_2026/7aav_11693.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7aav_11693/03_2026/7aav_11693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aav_11693/03_2026/7aav_11693.map" } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'TYR:plan': 21, 'GLU:plan': 65, 'GLN:plan1': 29, 'ASP:plan': 58, 'PHE:plan': 22, 'ASN:plan1': 25, 'ARG:plan': 38, 'HIS:plan': 15, 'TRP:plan': 3} 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: {'ARG:plan': 12, 'ASP:plan': 6, 'TRP:plan': 1, 'GLU:plan': 14, 'GLN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 4} 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: {'TRP:plan': 6, 'ARG:plan': 8, 'ASN:plan1': 2, 'GLU:plan': 10, 'ASP:plan': 3, 'TYR:plan': 3, 'GLN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 1} 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: {'ARG:plan': 4, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1} 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: {'ASN:plan1': 2, 'ASP:plan': 6, 'GLU:plan': 19, 'TYR:plan': 2, 'TRP:plan': 1, 'ARG:plan': 9, 'GLN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1} 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, 'TRP:plan': 11, 'HIS:plan': 17, 'TYR:plan': 8, 'ARG:plan': 18, 'GLU:plan': 10, 'ASN:plan1': 11, 'PHE:plan': 8, 'ASP:plan': 20} 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: {'TYR:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 2} 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: {'ASN:plan1': 7, 'ARG:plan': 11, 'ASP:plan': 9, 'HIS:plan': 4, 'GLN:plan1': 6, 'TYR:plan': 11, 'GLU:plan': 18, 'TRP:plan': 1, 'PHE:plan': 7} 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: {'GLU:plan': 92, 'ASP:plan': 98, 'HIS:plan': 38, 'ASN:plan1': 83, 'ARG:plan': 103, 'PHE:plan': 43, 'GLN:plan1': 66, 'TYR:plan': 40, 'TRP:plan': 17} 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: {'TRP:plan': 3, 'GLU:plan': 10, 'ASP:plan': 12, 'PHE:plan': 5, 'GLN:plan1': 5, 'ASN:plan1': 5, 'TYR:plan': 8, 'ARG:plan': 13, 'HIS:plan': 2} 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: {'ASP:plan': 9, 'GLN:plan1': 15, 'ARG:plan': 17, 'GLU:plan': 22, 'TYR:plan': 6, 'PHE:plan': 5, 'ASN:plan1': 7, 'HIS:plan': 3, 'TRP:plan': 3} 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: {'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 2, 'HIS:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 4, 'GLU:plan': 3} 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: {'GLU:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 7, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} 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: 6.35, per 1000 atoms: 0.25 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.3 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... Secondary structure from input PDB file: 127 helices and 33 sheets defined 39.2% alpha, 8.0% beta 41 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'r' and resid 118 through 125 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) Processing helix chain 'r' and resid 142 through 154 removed outlier: 3.643A pdb=" N ASP r 147 " --> pdb=" O THR r 143 " (cutoff:3.500A) Processing helix chain 'r' and resid 171 through 178 Processing helix chain 'r' and resid 208 through 210 No H-bonds generated for 'chain 'r' and resid 208 through 210' Processing helix chain 'r' and resid 211 through 220 removed outlier: 3.823A pdb=" N VAL r 215 " --> pdb=" O PHE r 211 " (cutoff:3.500A) Processing helix chain 'r' and resid 236 through 249 Processing helix chain 'r' and resid 261 through 266 Processing helix chain 'r' and resid 270 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 319 through 330 removed outlier: 3.641A pdb=" N ALA r 324 " --> pdb=" O LEU r 320 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR r 330 " --> pdb=" O ILE r 326 " (cutoff:3.500A) Processing helix chain 'r' and resid 368 through 373 Processing helix chain 'r' and resid 373 through 386 removed outlier: 3.560A pdb=" N VAL r 384 " --> pdb=" O ILE r 380 " (cutoff:3.500A) Processing helix chain 'r' and resid 391 through 399 Processing helix chain 'r' and resid 404 through 409 Processing helix chain 'r' and resid 411 through 424 Processing helix chain 'r' and resid 427 through 430 removed outlier: 4.084A pdb=" N PHE r 430 " --> pdb=" O PHE r 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 427 through 430' Processing helix chain 'r' and resid 431 through 436 Processing helix chain 'r' and resid 445 through 453 removed outlier: 3.538A pdb=" N ILE r 449 " --> pdb=" O ALA r 445 " (cutoff:3.500A) Processing helix chain 'r' and resid 460 through 465 Processing helix chain 'r' and resid 599 through 614 removed outlier: 3.590A pdb=" N MET r 603 " --> pdb=" O GLU r 599 " (cutoff:3.500A) Processing helix chain 'r' and resid 633 through 647 removed outlier: 3.584A pdb=" N ASP r 643 " --> pdb=" O CYS r 639 " (cutoff:3.500A) Processing helix chain 'r' and resid 693 through 702 Processing helix chain 'r' and resid 710 through 721 removed outlier: 3.514A pdb=" N PHE r 717 " --> pdb=" O LYS r 713 " (cutoff:3.500A) Processing helix chain 'r' and resid 725 through 731 removed outlier: 3.722A pdb=" N SER r 731 " --> pdb=" O LEU r 727 " (cutoff:3.500A) Processing helix chain 'r' and resid 736 through 740 removed outlier: 3.559A pdb=" N ALA r 739 " --> pdb=" O GLY r 736 " (cutoff:3.500A) Processing helix chain 'r' and resid 764 through 774 removed outlier: 3.871A pdb=" N GLN r 768 " --> pdb=" O ASP r 764 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR r 774 " --> pdb=" O PHE r 770 " (cutoff:3.500A) Processing helix chain 'r' and resid 807 through 822 Processing helix chain 'r' and resid 843 through 853 removed outlier: 3.509A pdb=" N ARG r 853 " --> pdb=" O VAL r 849 " (cutoff:3.500A) Processing helix chain 'r' and resid 882 through 891 removed outlier: 3.719A pdb=" N THR r 891 " --> pdb=" O LEU r 887 " (cutoff:3.500A) Processing helix chain 'r' and resid 928 through 937 removed outlier: 3.532A pdb=" N GLU r 932 " --> pdb=" O HIS r 928 " (cutoff:3.500A) Processing helix chain 'r' and resid 938 through 940 No H-bonds generated for 'chain 'r' and resid 938 through 940' Processing helix chain 'r' and resid 949 through 953 Processing helix chain 'Q' and resid 18 through 34 Processing helix chain 'Q' and resid 46 through 65 removed outlier: 3.682A pdb=" N ILE Q 60 " --> pdb=" O LYS Q 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 82 Processing helix chain 'Q' and resid 85 through 94 removed outlier: 4.045A pdb=" N LYS Q 94 " --> pdb=" O ALA Q 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 25 Processing helix chain 'L' and resid 30 through 39 removed outlier: 3.706A pdb=" N LEU L 37 " --> pdb=" O ARG L 33 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS L 39 " --> pdb=" O ALA L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 50 Processing helix chain 'L' and resid 64 through 78 removed outlier: 3.708A pdb=" N LYS L 76 " --> pdb=" O LEU L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 90 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 95 through 108 Processing helix chain 'R' and resid 217 through 224 Processing helix chain 'K' and resid 272 through 314 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) removed outlier: 3.914A pdb=" N GLU K 314 " --> pdb=" O LEU K 310 " (cutoff:3.500A) Processing helix chain '8' and resid 121 through 131 removed outlier: 3.506A pdb=" N ARG 8 130 " --> pdb=" O GLU 8 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 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 32 through 37 Processing helix chain 'I' and resid 43 through 54 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) removed outlier: 3.578A pdb=" N LEU I 54 " --> pdb=" O LYS I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 81 Processing helix chain 'I' and resid 83 through 93 Processing helix chain 'I' and resid 96 through 111 removed outlier: 3.560A pdb=" N ARG I 100 " --> pdb=" O PHE I 96 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR I 106 " --> pdb=" O LEU I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 121 removed outlier: 3.618A pdb=" N GLU I 121 " --> pdb=" O TYR I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 removed outlier: 3.541A pdb=" N ASN I 125 " --> pdb=" O PRO I 122 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP I 126 " --> pdb=" O LEU I 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 122 through 126' Processing helix chain 'I' and resid 144 through 152 Processing helix chain 'I' and resid 167 through 175 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 65 through 70 removed outlier: 3.560A pdb=" N ILE A 69 " --> pdb=" O HIS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 91 Processing helix chain 'A' and resid 94 through 105 removed outlier: 4.018A pdb=" N ALA A 98 " --> pdb=" O TYR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 158 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 210 through 215 removed outlier: 3.570A pdb=" N ARG A 214 " --> pdb=" O HIS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 243 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) Processing helix chain 'A' and resid 261 through 269 removed outlier: 4.191A pdb=" N THR A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 removed outlier: 3.540A pdb=" N LYS A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 321 removed outlier: 3.732A pdb=" N TYR A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 377 removed outlier: 3.798A pdb=" N ASP A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 398 through 406 removed outlier: 3.625A pdb=" N ALA A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 412 removed outlier: 3.935A pdb=" N ASN A 412 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 460 removed outlier: 3.705A pdb=" N ARG A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) 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) removed outlier: 4.121A pdb=" N LYS A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 489 through 512 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 534 through 539 removed outlier: 3.581A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 567 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 572 through 588 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 597 through 617 removed outlier: 3.741A pdb=" N GLN A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) 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 632 through 652 removed outlier: 3.619A pdb=" N VAL A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) 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 678 through 694 removed outlier: 3.515A pdb=" N ASP A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 722 removed outlier: 3.701A pdb=" N LEU A 710 " --> pdb=" O ALA A 706 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 722 " --> pdb=" O ARG A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 770 through 797 removed outlier: 3.537A pdb=" N LYS A 774 " --> pdb=" O THR A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 821 removed outlier: 4.093A pdb=" N ALA A 808 " --> pdb=" O GLU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 851 Processing helix chain 'A' and resid 857 through 872 removed outlier: 4.308A pdb=" N GLU A 862 " --> pdb=" O GLN A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 887 Processing helix chain 'A' and resid 912 through 934 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 948 through 961 removed outlier: 3.649A pdb=" N VAL A 952 " --> pdb=" O PRO A 948 " (cutoff:3.500A) 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 989 through 1001 Processing helix chain 'A' and resid 1002 through 1013 removed outlier: 3.536A pdb=" N TYR A1008 " --> pdb=" O ASN A1004 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN A1013 " --> pdb=" O MET A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1053 removed outlier: 3.805A pdb=" N ILE A1040 " --> pdb=" O PHE A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1063 Processing helix chain 'A' and resid 1076 through 1082 removed outlier: 3.891A pdb=" N GLU A1080 " --> pdb=" O ASP A1076 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1117 Processing helix chain 'A' and resid 1122 through 1126 removed outlier: 3.748A pdb=" N ILE A1125 " --> pdb=" O ASN A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1161 removed outlier: 3.645A pdb=" N VAL A1147 " --> pdb=" O MET A1143 " (cutoff:3.500A) 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) removed outlier: 3.809A pdb=" N LEU A1161 " --> pdb=" O ILE A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1250 Processing helix chain 'A' and resid 1255 through 1274 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 1281 through 1304 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 1318 removed outlier: 3.699A pdb=" N THR A1318 " --> pdb=" O VAL A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1339 Processing helix chain 'A' and resid 1374 through 1399 removed outlier: 3.678A pdb=" N ARG A1384 " --> pdb=" O ILE A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1422 Processing helix chain 'A' and resid 1426 through 1431 removed outlier: 3.534A pdb=" N ALA A1431 " --> pdb=" O ARG A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1447 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 1467 through 1479 removed outlier: 3.972A pdb=" N ARG A1471 " --> pdb=" O LEU A1467 " (cutoff:3.500A) 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 1479 through 1487 removed outlier: 3.713A pdb=" N HIS A1487 " --> pdb=" O GLY A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1494 removed outlier: 3.794A pdb=" N TYR A1494 " --> pdb=" O PHE A1490 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1538 Processing helix chain 'A' and resid 1538 through 1543 Processing helix chain 'A' and resid 1566 through 1577 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 1581 through 1600 removed outlier: 3.653A pdb=" N GLU A1600 " --> pdb=" O VAL A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1670 through 1674 removed outlier: 4.147A pdb=" N HIS A1674 " --> pdb=" O TYR A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1675 through 1687 removed outlier: 3.610A pdb=" N ARG A1681 " --> pdb=" O GLU A1677 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1735 removed outlier: 3.725A pdb=" N LYS A1732 " --> pdb=" O GLN A1728 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1752 Processing helix chain 'P' and resid 93 through 98 Processing helix chain 'P' and resid 146 through 151 removed outlier: 3.518A pdb=" N ALA P 151 " --> pdb=" O LEU P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 170 Processing helix chain 'P' and resid 175 through 179 removed outlier: 4.256A pdb=" N GLU P 178 " --> pdb=" O ARG P 175 " (cutoff:3.500A) Processing helix chain 'P' and resid 191 through 195 removed outlier: 3.754A pdb=" N ALA P 194 " --> pdb=" O ASP P 191 " (cutoff:3.500A) Processing helix chain 'P' and resid 197 through 203 removed outlier: 3.670A pdb=" N ARG P 201 " --> pdb=" O ASN P 197 " (cutoff:3.500A) Processing helix chain 'P' and resid 207 through 216 Processing helix chain 'v' and resid 136 through 162 Processing helix chain 'v' and resid 240 through 245 Processing helix chain 'v' and resid 281 through 326 removed outlier: 3.859A pdb=" N ALA v 285 " --> pdb=" O ASN v 281 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU v 300 " --> pdb=" O ARG v 296 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 100 removed outlier: 3.568A pdb=" N ILE N 99 " --> pdb=" O PHE N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 134 Processing helix chain 'q' and resid 23 through 36 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 38 through 40 No H-bonds generated for 'chain 'q' and resid 38 through 40' Processing sheet with id=AA1, first strand: chain 'r' and resid 184 through 187 Processing sheet with id=AA2, first strand: chain 'r' and resid 226 through 230 Processing sheet with id=AA3, first strand: chain 'r' and resid 310 through 311 Processing sheet with id=AA4, first strand: chain 'r' and resid 476 through 477 Processing sheet with id=AA5, first strand: chain 'r' and resid 482 through 483 Processing sheet with id=AA6, first strand: chain 'r' and resid 494 through 495 removed outlier: 3.509A pdb=" N GLY r 494 " --> pdb=" O VAL r 550 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'r' and resid 627 through 631 removed outlier: 4.114A pdb=" N HIS r 627 " --> pdb=" O VAL r 592 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'r' and resid 627 through 631 removed outlier: 4.114A pdb=" N HIS r 627 " --> pdb=" O VAL r 592 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'r' and resid 783 through 784 removed outlier: 3.518A pdb=" N THR r 665 " --> pdb=" O ARG r 826 " (cutoff:3.500A) Processing sheet with id=AB1, 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=AB2, first strand: chain 'r' and resid 857 through 862 removed outlier: 5.444A pdb=" N VAL r 857 " --> pdb=" O PHE r 874 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE r 874 " --> pdb=" O VAL r 857 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLU r 829 " --> pdb=" O TRP r 904 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N TRP r 904 " --> pdb=" O GLU r 829 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR r 831 " --> pdb=" O HIS r 902 " (cutoff:3.500A) Processing sheet with id=AB3, 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=AB4, 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=AB5, first strand: chain 'G' and resid 249 through 254 removed outlier: 3.709A pdb=" N TRP G 273 " --> pdb=" O LEU G 261 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS G 279 " --> pdb=" O ASP G 274 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 291 through 296 Processing sheet with id=AB7, first strand: chain 'G' and resid 333 through 337 removed outlier: 6.885A pdb=" N LEU G 356 " --> pdb=" O ARG G 365 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 416 through 421 removed outlier: 4.417A pdb=" N ALA G 431 " --> pdb=" O THR G 435 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N THR G 435 " --> pdb=" O ALA G 431 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL G 450 " --> pdb=" O MET G 436 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 60 through 61 Processing sheet with id=AC1, first strand: chain 'I' and resid 129 through 133 Processing sheet with id=AC2, first strand: chain 'A' and resid 127 through 128 Processing sheet with id=AC3, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AC4, first strand: chain 'A' and resid 516 through 518 Processing sheet with id=AC5, first strand: chain 'A' and resid 895 through 898 Processing sheet with id=AC6, first strand: chain 'A' and resid 1085 through 1090 removed outlier: 4.983A pdb=" N ILE A1085 " --> pdb=" O ARG A1100 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ARG A1100 " --> pdb=" O ILE A1085 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A1087 " --> pdb=" O PHE A1098 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1017 through 1018 removed outlier: 3.538A pdb=" N ILE A1017 " --> pdb=" O HIS A1024 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1185 through 1188 Processing sheet with id=AC9, first strand: chain 'A' and resid 1341 through 1342 Processing sheet with id=AD1, first strand: chain 'A' and resid 1606 through 1608 removed outlier: 6.998A pdb=" N PHE A1632 " --> pdb=" O GLU A1607 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR A1660 " --> pdb=" O LEU A1631 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 1642 through 1644 Processing sheet with id=AD3, 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=AD4, first strand: chain 'P' and resid 50 through 57 removed outlier: 8.239A pdb=" N ARG P 50 " --> pdb=" O LYS P 43 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LYS P 43 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N PHE P 52 " --> pdb=" O TYR P 41 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR P 41 " --> pdb=" O PHE P 52 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS P 38 " --> pdb=" O VAL v 200 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'q' and resid 2 through 7 Processing sheet with id=AD6, first strand: chain 'q' and resid 42 through 45 1116 hydrogen bonds defined for protein. 3225 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: 6.70 Time building geometry restraints manager: 3.26 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: 0.00 - 2.61: 37308 2.61 - 5.22: 552 5.22 - 7.83: 89 7.83 - 10.44: 12 10.44 - 13.06: 3 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: 15306 35.50 - 71.00: 445 71.00 - 106.50: 65 106.50 - 142.00: 13 142.00 - 177.50: 10 Dihedral angle restraints: 15839 sinusoidal: 4282 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 15836 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: 470 2.67 - 3.23: 22477 3.23 - 3.79: 38256 3.79 - 4.34: 43320 4.34 - 4.90: 69867 Nonbonded interactions: 174390 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 3.040 nonbonded pdb=" O SER r 183 " pdb=" OH TYR r 482 " model vdw 2.312 3.040 ... (remaining 174385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 29.410 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 26728 Z= 0.176 Angle : 0.781 13.055 37964 Z= 0.439 Chirality : 0.148 5.145 4800 Planarity : 0.006 0.077 4561 Dihedral : 17.514 177.497 8289 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.88 % Favored : 91.07 % Rotamer: Outliers : 0.18 % Allowed : 4.90 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 635 TYR 0.021 0.001 TYR A 94 PHE 0.015 0.001 PHE A 629 TRP 0.025 0.002 TRP A 720 HIS 0.007 0.001 HIS K 343 Details of bonding type rmsd covalent geometry : bond 0.00315 (26727) covalent geometry : angle 0.78089 (37964) hydrogen bonds : bond 0.27830 ( 1209) hydrogen bonds : angle 9.98215 ( 3391) Misc. bond : bond 0.00047 ( 1) *********************** 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 to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: K 336 LYS cc_start: 0.8283 (mttt) cc_final: 0.8073 (mttp) REVERT: K 378 MET cc_start: 0.6131 (mtt) cc_final: 0.5568 (mmp) REVERT: A 88 TYR cc_start: 0.8330 (t80) cc_final: 0.8072 (t80) REVERT: A 110 TRP cc_start: 0.8064 (p-90) cc_final: 0.7730 (p-90) REVERT: A 140 TYR cc_start: 0.9409 (t80) cc_final: 0.8996 (t80) REVERT: A 646 PRO cc_start: 0.9089 (Cg_endo) cc_final: 0.8803 (Cg_exo) REVERT: A 1128 TYR cc_start: 0.7640 (t80) cc_final: 0.7421 (t80) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.1689 time to fit residues: 64.7169 Evaluate side-chains 170 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 197 optimal weight: 0.0170 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.0670 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 overall best weight: 3.2162 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.094073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.078896 restraints weight = 115499.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.078637 restraints weight = 119895.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.079121 restraints weight = 105415.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.079102 restraints weight = 81431.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.079165 restraints weight = 77973.739| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26728 Z= 0.279 Angle : 0.766 11.460 37964 Z= 0.408 Chirality : 0.047 0.274 4800 Planarity : 0.006 0.079 4561 Dihedral : 18.456 174.429 6846 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.67 % Favored : 87.31 % Rotamer: Outliers : 0.35 % Allowed : 4.20 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.17 (0.11), residues: 3932 helix: -2.11 (0.10), residues: 1482 sheet: -2.81 (0.24), residues: 367 loop : -3.35 (0.12), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 344 TYR 0.023 0.002 TYR A1660 PHE 0.027 0.002 PHE r 430 TRP 0.027 0.002 TRP A 720 HIS 0.012 0.003 HIS r 903 Details of bonding type rmsd covalent geometry : bond 0.00540 (26727) covalent geometry : angle 0.76618 (37964) hydrogen bonds : bond 0.05091 ( 1209) hydrogen bonds : angle 5.15620 ( 3391) Misc. bond : bond 0.00210 ( 1) *********************** 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 172 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 TRP cc_start: 0.8170 (OUTLIER) cc_final: 0.7409 (m-10) REVERT: A 140 TYR cc_start: 0.9276 (t80) cc_final: 0.8821 (t80) REVERT: A 551 LEU cc_start: 0.9442 (mm) cc_final: 0.8636 (tt) REVERT: A 646 PRO cc_start: 0.9306 (Cg_endo) cc_final: 0.9020 (Cg_exo) REVERT: q 30 LEU cc_start: 0.9438 (mp) cc_final: 0.9165 (mt) outliers start: 2 outliers final: 0 residues processed: 170 average time/residue: 0.1371 time to fit residues: 41.1880 Evaluate side-chains 146 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 380 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 153 optimal weight: 20.0000 chunk 180 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 402 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 373 optimal weight: 2.9990 chunk 303 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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** ** K 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.092522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.077270 restraints weight = 115200.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.076690 restraints weight = 99829.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.076811 restraints weight = 99279.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.076972 restraints weight = 90594.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.076996 restraints weight = 85610.286| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 26728 Z= 0.242 Angle : 0.684 10.066 37964 Z= 0.362 Chirality : 0.045 0.307 4800 Planarity : 0.005 0.073 4561 Dihedral : 18.466 171.518 6846 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.92 % Favored : 87.05 % Rotamer: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.13), residues: 3932 helix: -0.40 (0.13), residues: 1487 sheet: -2.65 (0.25), residues: 359 loop : -3.20 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 158 TYR 0.022 0.002 TYR K 391 PHE 0.028 0.002 PHE r 430 TRP 0.022 0.002 TRP A 651 HIS 0.014 0.002 HIS r 903 Details of bonding type rmsd covalent geometry : bond 0.00473 (26727) covalent geometry : angle 0.68373 (37964) hydrogen bonds : bond 0.05110 ( 1209) hydrogen bonds : angle 4.86329 ( 3391) Misc. bond : bond 0.00154 ( 1) *********************** 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 163 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: K 340 LYS cc_start: 0.8398 (mtpt) cc_final: 0.8121 (mtpp) REVERT: A 140 TYR cc_start: 0.9280 (t80) cc_final: 0.8898 (t80) REVERT: A 551 LEU cc_start: 0.9470 (mm) cc_final: 0.8614 (tt) REVERT: A 646 PRO cc_start: 0.9351 (Cg_endo) cc_final: 0.9117 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1382 time to fit residues: 39.6088 Evaluate side-chains 143 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 350 optimal weight: 9.9990 chunk 333 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 374 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 196 optimal weight: 0.7980 chunk 140 optimal weight: 9.9990 chunk 166 optimal weight: 0.4980 chunk 248 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: r 902 HIS r 903 HIS ** K 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 HIS ** A1026 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.095043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.080374 restraints weight = 113897.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.079940 restraints weight = 110958.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.080107 restraints weight = 106636.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.080288 restraints weight = 91264.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.080334 restraints weight = 80378.147| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26728 Z= 0.119 Angle : 0.562 8.309 37964 Z= 0.286 Chirality : 0.042 0.272 4800 Planarity : 0.004 0.059 4561 Dihedral : 18.135 174.223 6846 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.14), residues: 3932 helix: 0.73 (0.14), residues: 1490 sheet: -2.47 (0.25), residues: 364 loop : -2.98 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 344 TYR 0.020 0.001 TYR K 391 PHE 0.018 0.001 PHE A 339 TRP 0.016 0.001 TRP A 637 HIS 0.012 0.001 HIS r 903 Details of bonding type rmsd covalent geometry : bond 0.00238 (26727) covalent geometry : angle 0.56175 (37964) hydrogen bonds : bond 0.03778 ( 1209) hydrogen bonds : angle 4.22450 ( 3391) Misc. bond : bond 0.00093 ( 1) *********************** 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 165 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: A 140 TYR cc_start: 0.9366 (t80) cc_final: 0.9006 (t80) REVERT: A 579 GLN cc_start: 0.8436 (tp40) cc_final: 0.7800 (tp40) REVERT: A 646 PRO cc_start: 0.9342 (Cg_endo) cc_final: 0.9048 (Cg_exo) REVERT: q 30 LEU cc_start: 0.9350 (mp) cc_final: 0.9116 (mt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1355 time to fit residues: 39.5073 Evaluate side-chains 144 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 244 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 chunk 247 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 314 optimal weight: 3.9990 chunk 363 optimal weight: 8.9990 chunk 111 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** ** r 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.090337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.075959 restraints weight = 115784.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.075469 restraints weight = 132286.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.075710 restraints weight = 117727.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.075816 restraints weight = 99719.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.075841 restraints weight = 91333.017| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 26728 Z= 0.293 Angle : 0.743 9.698 37964 Z= 0.395 Chirality : 0.048 0.371 4800 Planarity : 0.005 0.092 4561 Dihedral : 18.303 170.071 6846 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.90 % Favored : 84.10 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.14), residues: 3932 helix: 0.60 (0.14), residues: 1476 sheet: -2.22 (0.26), residues: 353 loop : -3.04 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 385 TYR 0.028 0.002 TYR A1445 PHE 0.024 0.002 PHE r 430 TRP 0.025 0.002 TRP A 651 HIS 0.012 0.003 HIS r 903 Details of bonding type rmsd covalent geometry : bond 0.00574 (26727) covalent geometry : angle 0.74316 (37964) hydrogen bonds : bond 0.05085 ( 1209) hydrogen bonds : angle 4.90873 ( 3391) Misc. bond : bond 0.00231 ( 1) *********************** 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 152 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.898 Fit side-chains REVERT: A 551 LEU cc_start: 0.9512 (mm) cc_final: 0.8587 (tt) REVERT: A 579 GLN cc_start: 0.8555 (tp40) cc_final: 0.8248 (tp40) REVERT: q 30 LEU cc_start: 0.9468 (mp) cc_final: 0.9253 (mt) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1391 time to fit residues: 37.2309 Evaluate side-chains 138 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 67 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 362 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 355 optimal weight: 0.0570 chunk 391 optimal weight: 4.9990 chunk 379 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 179 optimal weight: 0.0370 chunk 33 optimal weight: 1.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: r 902 HIS r 903 HIS ** K 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.094768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.080360 restraints weight = 114632.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.080781 restraints weight = 128856.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.080504 restraints weight = 88191.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.080197 restraints weight = 92143.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.080312 restraints weight = 85383.705| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 26728 Z= 0.103 Angle : 0.563 8.323 37964 Z= 0.285 Chirality : 0.042 0.279 4800 Planarity : 0.004 0.053 4561 Dihedral : 17.976 174.603 6846 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.14), residues: 3932 helix: 1.38 (0.14), residues: 1488 sheet: -2.17 (0.25), residues: 375 loop : -2.82 (0.14), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 419 TYR 0.020 0.001 TYR K 391 PHE 0.016 0.001 PHE A 339 TRP 0.020 0.001 TRP A 651 HIS 0.009 0.001 HIS r 903 Details of bonding type rmsd covalent geometry : bond 0.00207 (26727) covalent geometry : angle 0.56318 (37964) hydrogen bonds : bond 0.03594 ( 1209) hydrogen bonds : angle 4.02927 ( 3391) Misc. bond : bond 0.00054 ( 1) *********************** 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 170 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.861 Fit side-chains REVERT: A 97 HIS cc_start: 0.8095 (t70) cc_final: 0.7889 (t-90) REVERT: A 140 TYR cc_start: 0.9344 (t80) cc_final: 0.8972 (t80) REVERT: A 424 ILE cc_start: 0.9163 (mm) cc_final: 0.8911 (mm) REVERT: A 579 GLN cc_start: 0.8342 (tp40) cc_final: 0.7752 (tp40) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1478 time to fit residues: 43.2023 Evaluate side-chains 145 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 309 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 181 optimal weight: 9.9990 chunk 280 optimal weight: 0.6980 chunk 327 optimal weight: 0.8980 chunk 355 optimal weight: 1.9990 chunk 404 optimal weight: 0.0670 chunk 31 optimal weight: 0.9990 chunk 267 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 chunk 343 optimal weight: 0.0000 overall best weight: 0.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.095727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.081192 restraints weight = 114050.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.080736 restraints weight = 91259.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.080691 restraints weight = 85548.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.080785 restraints weight = 79172.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.080809 restraints weight = 76686.037| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26728 Z= 0.098 Angle : 0.543 8.549 37964 Z= 0.272 Chirality : 0.042 0.298 4800 Planarity : 0.004 0.053 4561 Dihedral : 17.701 174.227 6846 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.14), residues: 3932 helix: 1.78 (0.14), residues: 1488 sheet: -2.07 (0.25), residues: 381 loop : -2.67 (0.14), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 388 TYR 0.011 0.001 TYR A 140 PHE 0.017 0.001 PHE K 337 TRP 0.023 0.001 TRP A1263 HIS 0.006 0.001 HIS r 903 Details of bonding type rmsd covalent geometry : bond 0.00198 (26727) covalent geometry : angle 0.54297 (37964) hydrogen bonds : bond 0.03369 ( 1209) hydrogen bonds : angle 3.68805 ( 3391) Misc. bond : bond 0.00027 ( 1) *********************** 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 168 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.921 Fit side-chains REVERT: A 140 TYR cc_start: 0.9353 (t80) cc_final: 0.9034 (t80) REVERT: A 579 GLN cc_start: 0.8431 (tp40) cc_final: 0.7770 (tp40) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1374 time to fit residues: 41.2412 Evaluate side-chains 151 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 71 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 159 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 262 optimal weight: 7.9990 chunk 298 optimal weight: 0.9990 chunk 364 optimal weight: 30.0000 chunk 183 optimal weight: 0.7980 chunk 311 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 177 optimal weight: 20.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.093789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.078859 restraints weight = 114944.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.078782 restraints weight = 127452.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.079130 restraints weight = 105039.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.078984 restraints weight = 89243.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.079077 restraints weight = 83413.781| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26728 Z= 0.155 Angle : 0.583 8.601 37964 Z= 0.298 Chirality : 0.043 0.313 4800 Planarity : 0.004 0.054 4561 Dihedral : 17.778 173.272 6846 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.08 % Favored : 87.92 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.14), residues: 3932 helix: 1.77 (0.15), residues: 1488 sheet: -2.00 (0.25), residues: 381 loop : -2.66 (0.14), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 663 TYR 0.010 0.001 TYR A1660 PHE 0.024 0.001 PHE K 337 TRP 0.021 0.001 TRP A1263 HIS 0.011 0.002 HIS r 902 Details of bonding type rmsd covalent geometry : bond 0.00309 (26727) covalent geometry : angle 0.58301 (37964) hydrogen bonds : bond 0.03682 ( 1209) hydrogen bonds : angle 3.86960 ( 3391) Misc. bond : bond 0.00068 ( 1) *********************** 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 160 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.991 Fit side-chains REVERT: A 551 LEU cc_start: 0.9377 (mm) cc_final: 0.8520 (tt) REVERT: A 579 GLN cc_start: 0.8444 (tp40) cc_final: 0.8208 (tp40) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1377 time to fit residues: 39.1832 Evaluate side-chains 142 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 179 optimal weight: 3.9990 chunk 2 optimal weight: 0.1980 chunk 171 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 350 optimal weight: 10.0000 chunk 317 optimal weight: 0.0570 chunk 45 optimal weight: 0.5980 chunk 126 optimal weight: 0.9990 chunk 83 optimal weight: 0.0980 chunk 162 optimal weight: 9.9990 overall best weight: 0.3900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS ** 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 = 0.3592 r_free = 0.3592 target = 0.096510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.081667 restraints weight = 114470.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.081479 restraints weight = 122457.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.081900 restraints weight = 98791.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.081772 restraints weight = 82044.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.081906 restraints weight = 76823.930| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26728 Z= 0.090 Angle : 0.538 8.538 37964 Z= 0.268 Chirality : 0.041 0.284 4800 Planarity : 0.004 0.058 4561 Dihedral : 17.631 175.218 6846 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.15), residues: 3932 helix: 2.00 (0.15), residues: 1489 sheet: -1.87 (0.25), residues: 400 loop : -2.57 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 152 TYR 0.018 0.001 TYR K 391 PHE 0.021 0.001 PHE K 337 TRP 0.026 0.001 TRP A1263 HIS 0.004 0.001 HIS Q 54 Details of bonding type rmsd covalent geometry : bond 0.00182 (26727) covalent geometry : angle 0.53755 (37964) hydrogen bonds : bond 0.03185 ( 1209) hydrogen bonds : angle 3.54481 ( 3391) Misc. bond : bond 0.00028 ( 1) *********************** 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 169 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 140 TYR cc_start: 0.9361 (t80) cc_final: 0.9015 (t80) REVERT: A 579 GLN cc_start: 0.8291 (tp40) cc_final: 0.7659 (tp40) REVERT: A 1494 TYR cc_start: 0.6172 (m-10) cc_final: 0.5936 (m-80) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1365 time to fit residues: 40.6039 Evaluate side-chains 150 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 320 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 210 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 233 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 339 optimal weight: 0.9990 chunk 153 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.094259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.079667 restraints weight = 114714.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.079319 restraints weight = 127546.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.079767 restraints weight = 119114.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.079795 restraints weight = 88155.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.079819 restraints weight = 82783.250| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26728 Z= 0.146 Angle : 0.569 8.735 37964 Z= 0.290 Chirality : 0.043 0.314 4800 Planarity : 0.004 0.058 4561 Dihedral : 17.706 173.772 6846 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.14), residues: 3932 helix: 1.90 (0.14), residues: 1489 sheet: -1.78 (0.25), residues: 399 loop : -2.58 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 152 TYR 0.016 0.001 TYR q 60 PHE 0.024 0.001 PHE K 337 TRP 0.026 0.001 TRP A1263 HIS 0.007 0.001 HIS q 54 Details of bonding type rmsd covalent geometry : bond 0.00291 (26727) covalent geometry : angle 0.56945 (37964) hydrogen bonds : bond 0.03579 ( 1209) hydrogen bonds : angle 3.72861 ( 3391) Misc. bond : bond 0.00043 ( 1) ********************** 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 156 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.945 Fit side-chains REVERT: A 551 LEU cc_start: 0.9355 (mm) cc_final: 0.8498 (tt) REVERT: A 579 GLN cc_start: 0.8487 (tp40) cc_final: 0.8189 (tp40) REVERT: A 1494 TYR cc_start: 0.6173 (m-10) cc_final: 0.5860 (m-80) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1336 time to fit residues: 37.2237 Evaluate side-chains 143 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 407 random chunks: chunk 280 optimal weight: 3.9990 chunk 145 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 95 optimal weight: 9.9990 chunk 399 optimal weight: 5.9990 chunk 297 optimal weight: 0.8980 chunk 188 optimal weight: 0.7980 chunk 237 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.090834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.077166 restraints weight = 115582.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.076973 restraints weight = 149134.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.076203 restraints weight = 106767.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.076174 restraints weight = 108023.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.076271 restraints weight = 98518.273| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 26728 Z= 0.245 Angle : 0.685 9.964 37964 Z= 0.360 Chirality : 0.046 0.315 4800 Planarity : 0.005 0.070 4561 Dihedral : 18.097 171.791 6846 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.88 % Favored : 85.12 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.14), residues: 3932 helix: 1.44 (0.14), residues: 1455 sheet: -1.84 (0.25), residues: 390 loop : -2.70 (0.14), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 419 TYR 0.023 0.002 TYR r 327 PHE 0.021 0.002 PHE r 490 TRP 0.033 0.002 TRP A 651 HIS 0.009 0.002 HIS A1615 Details of bonding type rmsd covalent geometry : bond 0.00480 (26727) covalent geometry : angle 0.68458 (37964) hydrogen bonds : bond 0.04569 ( 1209) hydrogen bonds : angle 4.47069 ( 3391) Misc. bond : bond 0.00145 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3396.50 seconds wall clock time: 59 minutes 4.67 seconds (3544.67 seconds total)