Starting phenix.real_space_refine on Fri Feb 23 01:12:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x43_22039/02_2024/6x43_22039_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x43_22039/02_2024/6x43_22039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x43_22039/02_2024/6x43_22039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x43_22039/02_2024/6x43_22039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x43_22039/02_2024/6x43_22039_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x43_22039/02_2024/6x43_22039_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.006 sd= 1.083 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 113 5.49 5 Mg 2 5.21 5 S 142 5.16 5 C 22295 2.51 5 N 6395 2.21 5 O 7106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 33": "OE1" <-> "OE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A GLU 800": "OE1" <-> "OE2" Residue "A GLU 872": "OE1" <-> "OE2" Residue "A GLU 931": "OE1" <-> "OE2" Residue "A GLU 937": "OE1" <-> "OE2" Residue "A GLU 962": "OE1" <-> "OE2" Residue "A GLU 1036": "OE1" <-> "OE2" Residue "A GLU 1045": "OE1" <-> "OE2" Residue "A GLU 1143": "OE1" <-> "OE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G GLU 72": "OE1" <-> "OE2" Residue "G GLU 76": "OE1" <-> "OE2" Residue "G GLU 136": "OE1" <-> "OE2" Residue "G GLU 215": "OE1" <-> "OE2" Residue "H GLU 29": "OE1" <-> "OE2" Residue "H GLU 67": "OE1" <-> "OE2" Residue "H GLU 214": "OE1" <-> "OE2" Residue "I GLU 7": "OE1" <-> "OE2" Residue "I GLU 40": "OE1" <-> "OE2" Residue "I TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 218": "OE1" <-> "OE2" Residue "I GLU 244": "OE1" <-> "OE2" Residue "I ARG 268": "NH1" <-> "NH2" Residue "I GLU 286": "OE1" <-> "OE2" Residue "I GLU 290": "OE1" <-> "OE2" Residue "I GLU 308": "OE1" <-> "OE2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I GLU 334": "OE1" <-> "OE2" Residue "I GLU 374": "OE1" <-> "OE2" Residue "I GLU 413": "OE1" <-> "OE2" Residue "I GLU 546": "OE1" <-> "OE2" Residue "I GLU 625": "OE1" <-> "OE2" Residue "I GLU 778": "OE1" <-> "OE2" Residue "I GLU 835": "OE1" <-> "OE2" Residue "I GLU 867": "OE1" <-> "OE2" Residue "I GLU 940": "OE1" <-> "OE2" Residue "I GLU 949": "OE1" <-> "OE2" Residue "I GLU 950": "OE1" <-> "OE2" Residue "I GLU 962": "OE1" <-> "OE2" Residue "I GLU 999": "OE1" <-> "OE2" Residue "I GLU 1024": "OE1" <-> "OE2" Residue "I GLU 1143": "OE1" <-> "OE2" Residue "I GLU 1167": "OE1" <-> "OE2" Residue "I GLU 1197": "OE1" <-> "OE2" Residue "I GLU 1289": "OE1" <-> "OE2" Residue "I GLU 1321": "OE1" <-> "OE2" Residue "J GLU 69": "OE1" <-> "OE2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J GLU 163": "OE1" <-> "OE2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J GLU 171": "OE1" <-> "OE2" Residue "J GLU 195": "OE1" <-> "OE2" Residue "J GLU 199": "OE1" <-> "OE2" Residue "J GLU 203": "OE1" <-> "OE2" Residue "J GLU 225": "OE1" <-> "OE2" Residue "J GLU 295": "OE1" <-> "OE2" Residue "J PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 386": "OE1" <-> "OE2" Residue "J GLU 405": "OE1" <-> "OE2" Residue "J GLU 414": "OE1" <-> "OE2" Residue "J GLU 418": "OE1" <-> "OE2" Residue "J GLU 479": "OE1" <-> "OE2" Residue "J GLU 497": "OE1" <-> "OE2" Residue "J GLU 658": "OE1" <-> "OE2" Residue "J GLU 660": "OE1" <-> "OE2" Residue "J GLU 663": "OE1" <-> "OE2" Residue "J GLU 666": "OE1" <-> "OE2" Residue "J GLU 677": "OE1" <-> "OE2" Residue "J GLU 704": "OE1" <-> "OE2" Residue "J GLU 714": "OE1" <-> "OE2" Residue "J GLU 827": "OE1" <-> "OE2" Residue "J GLU 833": "OE1" <-> "OE2" Residue "J GLU 846": "OE1" <-> "OE2" Residue "J GLU 873": "OE1" <-> "OE2" Residue "J GLU 874": "OE1" <-> "OE2" Residue "J GLU 913": "OE1" <-> "OE2" Residue "J GLU 981": "OE1" <-> "OE2" Residue "J GLU 1015": "OE1" <-> "OE2" Residue "J GLU 1030": "OE1" <-> "OE2" Residue "J GLU 1052": "OE1" <-> "OE2" Residue "J GLU 1066": "OE1" <-> "OE2" Residue "J GLU 1146": "OE1" <-> "OE2" Residue "J GLU 1168": "OE1" <-> "OE2" Residue "J GLU 1276": "OE1" <-> "OE2" Residue "J GLU 1327": "OE1" <-> "OE2" Residue "J TYR 1365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 55": "OE1" <-> "OE2" Residue "K GLU 74": "OE1" <-> "OE2" Residue "K GLU 76": "OE1" <-> "OE2" Residue "K GLU 79": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36055 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 8982 Classifications: {'peptide': 1144} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 55, 'TRANS': 1088} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 10, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 108 Chain: "G" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1725 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1667 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 10354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10354 Classifications: {'peptide': 1316} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "J" Number of atoms: 10383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10383 Classifications: {'peptide': 1336} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1280} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Chain: "P" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1050 Classifications: {'DNA': 52} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 51} Chain breaks: 1 Chain: "Q" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1011 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23177 SG CYS J 70 25.219 93.395 101.684 1.00 98.41 S ATOM 23191 SG CYS J 72 24.700 96.981 100.720 1.00102.52 S ATOM 23299 SG CYS J 85 22.471 94.165 99.254 1.00104.97 S ATOM 23323 SG CYS J 88 26.183 94.049 98.464 1.00100.42 S ATOM 28999 SG CYS J 814 53.429 33.493 106.376 1.00 64.15 S ATOM 29564 SG CYS J 888 54.097 36.979 105.187 1.00 59.64 S ATOM 29636 SG CYS J 898 55.991 34.004 107.900 1.00 55.45 S Time building chain proxies: 19.66, per 1000 atoms: 0.55 Number of scatterers: 36055 At special positions: 0 Unit cell: (137.8, 193.7, 195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 142 16.00 P 113 15.00 Mg 2 11.99 O 7106 8.00 N 6395 7.00 C 22295 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.09 Conformation dependent library (CDL) restraints added in 6.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " Number of angles added : 6 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 142 helices and 42 sheets defined 32.2% alpha, 11.1% beta 49 base pairs and 85 stacking pairs defined. Time for finding SS restraints: 17.61 Creating SS restraints... Processing helix chain 'A' and resid 27 through 37 Processing helix chain 'A' and resid 49 through 62 removed outlier: 4.167A pdb=" N SER A 60 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 100 removed outlier: 4.143A pdb=" N SER A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Proline residue: A 99 - end of helix Processing helix chain 'A' and resid 110 through 113 No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 139 through 147 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 291 through 305 Processing helix chain 'A' and resid 317 through 320 No H-bonds generated for 'chain 'A' and resid 317 through 320' Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 393 through 399 Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 514 through 516 No H-bonds generated for 'chain 'A' and resid 514 through 516' Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 549 through 554 removed outlier: 4.516A pdb=" N ARG A 554 " --> pdb=" O TRP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 577 Processing helix chain 'A' and resid 587 through 595 removed outlier: 4.336A pdb=" N PHE A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 616 Processing helix chain 'A' and resid 634 through 648 removed outlier: 3.500A pdb=" N ALA A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 644 " --> pdb=" O ARG A 640 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 672 Processing helix chain 'A' and resid 689 through 701 removed outlier: 3.691A pdb=" N THR A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLN A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA A 697 " --> pdb=" O THR A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 714 Processing helix chain 'A' and resid 737 through 745 removed outlier: 4.336A pdb=" N ILE A 742 " --> pdb=" O HIS A 738 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS A 743 " --> pdb=" O LYS A 739 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET A 745 " --> pdb=" O ARG A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 767 removed outlier: 3.981A pdb=" N ALA A 766 " --> pdb=" O THR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 808 removed outlier: 3.552A pdb=" N ARG A 808 " --> pdb=" O ARG A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 832 Processing helix chain 'A' and resid 848 through 858 removed outlier: 3.784A pdb=" N ARG A 852 " --> pdb=" O ARG A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 871 No H-bonds generated for 'chain 'A' and resid 869 through 871' Processing helix chain 'A' and resid 893 through 902 Processing helix chain 'A' and resid 919 through 921 No H-bonds generated for 'chain 'A' and resid 919 through 921' Processing helix chain 'A' and resid 924 through 935 Processing helix chain 'A' and resid 942 through 949 Processing helix chain 'A' and resid 972 through 989 removed outlier: 3.790A pdb=" N GLU A 977 " --> pdb=" O SER A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 999 Processing helix chain 'A' and resid 1020 through 1031 Processing helix chain 'A' and resid 1036 through 1050 Processing helix chain 'A' and resid 1055 through 1073 removed outlier: 3.698A pdb=" N LYS A1072 " --> pdb=" O GLN A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1106 Processing helix chain 'A' and resid 1128 through 1144 Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 78 through 87 removed outlier: 4.162A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 213 through 228 Processing helix chain 'H' and resid 35 through 49 removed outlier: 4.244A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 87 removed outlier: 4.028A pdb=" N ASN H 84 " --> pdb=" O GLU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 213 through 226 Processing helix chain 'I' and resid 29 through 38 Processing helix chain 'I' and resid 48 through 56 Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.793A pdb=" N LEU I 213 " --> pdb=" O ILE I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 243 through 246 Processing helix chain 'I' and resid 271 through 279 Processing helix chain 'I' and resid 319 through 327 Processing helix chain 'I' and resid 348 through 353 Processing helix chain 'I' and resid 360 through 370 Processing helix chain 'I' and resid 378 through 389 removed outlier: 3.988A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 422 through 437 Processing helix chain 'I' and resid 456 through 480 removed outlier: 3.652A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 484 through 486 No H-bonds generated for 'chain 'I' and resid 484 through 486' Processing helix chain 'I' and resid 496 through 507 removed outlier: 3.591A pdb=" N ALA I 501 " --> pdb=" O PRO I 497 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE I 505 " --> pdb=" O ALA I 501 " (cutoff:3.500A) Processing helix chain 'I' and resid 520 through 527 Processing helix chain 'I' and resid 552 through 554 No H-bonds generated for 'chain 'I' and resid 552 through 554' Processing helix chain 'I' and resid 610 through 613 No H-bonds generated for 'chain 'I' and resid 610 through 613' Processing helix chain 'I' and resid 647 through 649 No H-bonds generated for 'chain 'I' and resid 647 through 649' Processing helix chain 'I' and resid 671 through 673 No H-bonds generated for 'chain 'I' and resid 671 through 673' Processing helix chain 'I' and resid 676 through 688 removed outlier: 4.075A pdb=" N GLN I 688 " --> pdb=" O ASN I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 711 Processing helix chain 'I' and resid 821 through 824 No H-bonds generated for 'chain 'I' and resid 821 through 824' Processing helix chain 'I' and resid 859 through 862 No H-bonds generated for 'chain 'I' and resid 859 through 862' Processing helix chain 'I' and resid 943 through 978 Processing helix chain 'I' and resid 986 through 991 removed outlier: 3.794A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) Processing helix chain 'I' and resid 1006 through 1037 Processing helix chain 'I' and resid 1082 through 1084 No H-bonds generated for 'chain 'I' and resid 1082 through 1084' Processing helix chain 'I' and resid 1101 through 1104 No H-bonds generated for 'chain 'I' and resid 1101 through 1104' Processing helix chain 'I' and resid 1110 through 1133 Processing helix chain 'I' and resid 1138 through 1149 removed outlier: 3.803A pdb=" N GLU I1143 " --> pdb=" O ALA I1139 " (cutoff:3.500A) Processing helix chain 'I' and resid 1161 through 1163 No H-bonds generated for 'chain 'I' and resid 1161 through 1163' Processing helix chain 'I' and resid 1168 through 1175 Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1273 through 1280 removed outlier: 3.514A pdb=" N LEU I1278 " --> pdb=" O GLU I1274 " (cutoff:3.500A) Processing helix chain 'I' and resid 1284 through 1291 Processing helix chain 'I' and resid 1298 through 1309 removed outlier: 3.614A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) Processing helix chain 'I' and resid 1321 through 1331 removed outlier: 3.589A pdb=" N LEU I1326 " --> pdb=" O SER I1322 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 95 through 99 Processing helix chain 'J' and resid 123 through 128 Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 162 through 171 Processing helix chain 'J' and resid 182 through 190 Processing helix chain 'J' and resid 194 through 206 Processing helix chain 'J' and resid 213 through 229 Processing helix chain 'J' and resid 234 through 236 No H-bonds generated for 'chain 'J' and resid 234 through 236' Processing helix chain 'J' and resid 264 through 284 Processing helix chain 'J' and resid 289 through 307 removed outlier: 3.745A pdb=" N ASN J 294 " --> pdb=" O ILE J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 337 through 340 No H-bonds generated for 'chain 'J' and resid 337 through 340' Processing helix chain 'J' and resid 370 through 376 Processing helix chain 'J' and resid 378 through 388 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 406 through 415 removed outlier: 4.149A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 433 No H-bonds generated for 'chain 'J' and resid 431 through 433' Processing helix chain 'J' and resid 454 through 457 No H-bonds generated for 'chain 'J' and resid 454 through 457' Processing helix chain 'J' and resid 474 through 483 Processing helix chain 'J' and resid 506 through 513 Processing helix chain 'J' and resid 530 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.964A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 589 through 591 No H-bonds generated for 'chain 'J' and resid 589 through 591' Processing helix chain 'J' and resid 599 through 612 Processing helix chain 'J' and resid 615 through 635 Processing helix chain 'J' and resid 641 through 643 No H-bonds generated for 'chain 'J' and resid 641 through 643' Processing helix chain 'J' and resid 650 through 669 Processing helix chain 'J' and resid 675 through 702 Processing helix chain 'J' and resid 721 through 727 Processing helix chain 'J' and resid 734 through 740 Processing helix chain 'J' and resid 769 through 803 removed outlier: 4.095A pdb=" N LYS J 781 " --> pdb=" O HIS J 777 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY J 782 " --> pdb=" O GLY J 778 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU J 783 " --> pdb=" O ALA J 779 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 838 No H-bonds generated for 'chain 'J' and resid 835 through 838' Processing helix chain 'J' and resid 866 through 875 Processing helix chain 'J' and resid 896 through 899 No H-bonds generated for 'chain 'J' and resid 896 through 899' Processing helix chain 'J' and resid 915 through 924 Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1138 through 1145 Processing helix chain 'J' and resid 1217 through 1224 Processing helix chain 'J' and resid 1226 through 1243 removed outlier: 3.948A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) Processing helix chain 'J' and resid 1251 through 1260 removed outlier: 3.520A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1291 removed outlier: 3.701A pdb=" N GLU J1291 " --> pdb=" O ILE J1287 " (cutoff:3.500A) Processing helix chain 'J' and resid 1309 through 1314 removed outlier: 3.575A pdb=" N SER J1313 " --> pdb=" O ILE J1309 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU J1314 " --> pdb=" O THR J1310 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 1309 through 1314' Processing helix chain 'J' and resid 1328 through 1337 Processing helix chain 'J' and resid 1349 through 1352 No H-bonds generated for 'chain 'J' and resid 1349 through 1352' Processing helix chain 'J' and resid 1363 through 1371 Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 46 through 55 Processing helix chain 'K' and resid 61 through 77 Processing sheet with id= A, first strand: chain 'A' and resid 336 through 339 Processing sheet with id= B, first strand: chain 'A' and resid 282 through 284 removed outlier: 5.921A pdb=" N VAL A 43 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 127 through 130 Processing sheet with id= D, first strand: chain 'A' and resid 161 through 165 Processing sheet with id= E, first strand: chain 'A' and resid 434 through 436 Processing sheet with id= F, first strand: chain 'A' and resid 529 through 531 removed outlier: 5.569A pdb=" N MET A 510 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N MET A 496 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TYR A 508 " --> pdb=" O MET A 496 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR A 498 " --> pdb=" O GLY A 506 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY A 506 " --> pdb=" O THR A 498 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 623 through 625 removed outlier: 6.830A pdb=" N ILE A 751 " --> pdb=" O ARG A 624 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 725 through 729 Processing sheet with id= I, first strand: chain 'A' and resid 787 through 792 removed outlier: 3.696A pdb=" N ARG A 791 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 883 " --> pdb=" O TYR A 911 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLN A 811 " --> pdb=" O ASN A 881 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE A 883 " --> pdb=" O GLN A 811 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TYR A 813 " --> pdb=" O ILE A 883 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE A 885 " --> pdb=" O TYR A 813 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A 815 " --> pdb=" O ILE A 885 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1111 through 1113 Processing sheet with id= K, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.883A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.671A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.742A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 15 through 17 Processing sheet with id= O, first strand: chain 'H' and resid 97 through 101 removed outlier: 3.765A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 66 through 70 removed outlier: 3.660A pdb=" N GLU I 67 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 73 through 75 Processing sheet with id= R, first strand: chain 'I' and resid 93 through 95 removed outlier: 3.540A pdb=" N ILE I 127 " --> pdb=" O ALA I 94 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= T, first strand: chain 'I' and resid 148 through 151 removed outlier: 3.551A pdb=" N GLN I 148 " --> pdb=" O ARG I 454 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 154 through 160 removed outlier: 4.029A pdb=" N ASP I 160 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 228 through 231 Processing sheet with id= W, first strand: chain 'I' and resid 238 through 240 Processing sheet with id= X, first strand: chain 'I' and resid 603 through 606 Processing sheet with id= Y, first strand: chain 'I' and resid 633 through 637 Processing sheet with id= Z, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.218A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 1226 through 1232 removed outlier: 4.437A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.819A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'I' and resid 301 through 303 removed outlier: 5.774A pdb=" N ASP I 303 " --> pdb=" O LEU I 309 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU I 309 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'I' and resid 816 through 819 removed outlier: 7.220A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.756A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 103 through 106 removed outlier: 3.571A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= AH, first strand: chain 'J' and resid 547 through 556 Processing sheet with id= AI, first strand: chain 'J' and resid 820 through 823 Processing sheet with id= AJ, first strand: chain 'J' and resid 957 through 961 Processing sheet with id= AK, first strand: chain 'J' and resid 965 through 967 Processing sheet with id= AL, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id= AM, first strand: chain 'J' and resid 1046 through 1048 removed outlier: 3.528A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id= AO, first strand: chain 'J' and resid 1279 through 1281 Processing sheet with id= AP, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.645A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) 1070 hydrogen bonds defined for protein. 3093 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 124 hydrogen bonds 240 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 85 stacking parallelities Total time for adding SS restraints: 15.05 Time building geometry restraints manager: 15.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6209 1.32 - 1.44: 9378 1.44 - 1.57: 20808 1.57 - 1.69: 221 1.69 - 1.81: 249 Bond restraints: 36865 Sorted by residual: bond pdb=" C4 ATP A2000 " pdb=" C5 ATP A2000 " ideal model delta sigma weight residual 1.388 1.453 -0.065 1.00e-02 1.00e+04 4.26e+01 bond pdb=" C4 ATP A2000 " pdb=" N9 ATP A2000 " ideal model delta sigma weight residual 1.374 1.317 0.057 1.00e-02 1.00e+04 3.19e+01 bond pdb=" C5 ATP A2000 " pdb=" C6 ATP A2000 " ideal model delta sigma weight residual 1.409 1.465 -0.056 1.00e-02 1.00e+04 3.18e+01 bond pdb=" CA HIS A 120 " pdb=" C HIS A 120 " ideal model delta sigma weight residual 1.529 1.478 0.052 9.30e-03 1.16e+04 3.07e+01 bond pdb=" C5 ATP A2000 " pdb=" N7 ATP A2000 " ideal model delta sigma weight residual 1.387 1.332 0.055 1.00e-02 1.00e+04 3.05e+01 ... (remaining 36860 not shown) Histogram of bond angle deviations from ideal: 92.01 - 100.79: 124 100.79 - 109.58: 6087 109.58 - 118.36: 23221 118.36 - 127.14: 20376 127.14 - 135.93: 523 Bond angle restraints: 50331 Sorted by residual: angle pdb=" PB ATP A2000 " pdb=" O3B ATP A2000 " pdb=" PG ATP A2000 " ideal model delta sigma weight residual 139.87 118.23 21.64 1.00e+00 1.00e+00 4.68e+02 angle pdb=" PA ATP A2000 " pdb=" O3A ATP A2000 " pdb=" PB ATP A2000 " ideal model delta sigma weight residual 136.83 116.04 20.79 1.00e+00 1.00e+00 4.32e+02 angle pdb=" N VAL G 14 " pdb=" CA VAL G 14 " pdb=" C VAL G 14 " ideal model delta sigma weight residual 110.72 124.07 -13.35 1.01e+00 9.80e-01 1.75e+02 angle pdb=" N VAL I1186 " pdb=" CA VAL I1186 " pdb=" C VAL I1186 " ideal model delta sigma weight residual 110.42 120.26 -9.84 9.60e-01 1.09e+00 1.05e+02 angle pdb=" N LEU A 474 " pdb=" CA LEU A 474 " pdb=" C LEU A 474 " ideal model delta sigma weight residual 109.15 95.62 13.53 1.44e+00 4.82e-01 8.83e+01 ... (remaining 50326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.25: 21498 35.25 - 70.50: 794 70.50 - 105.75: 47 105.75 - 141.00: 2 141.00 - 176.24: 1 Dihedral angle restraints: 22342 sinusoidal: 9913 harmonic: 12429 Sorted by residual: dihedral pdb=" CA GLY J 852 " pdb=" C GLY J 852 " pdb=" N THR J 853 " pdb=" CA THR J 853 " ideal model delta harmonic sigma weight residual -180.00 -150.41 -29.59 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA SER I1295 " pdb=" C SER I1295 " pdb=" N ASP I1296 " pdb=" CA ASP I1296 " ideal model delta harmonic sigma weight residual -180.00 -151.70 -28.30 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA ASN I 235 " pdb=" C ASN I 235 " pdb=" N LYS I 236 " pdb=" CA LYS I 236 " ideal model delta harmonic sigma weight residual 180.00 152.38 27.62 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 22339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 5057 0.088 - 0.176: 623 0.176 - 0.264: 43 0.264 - 0.352: 9 0.352 - 0.440: 7 Chirality restraints: 5739 Sorted by residual: chirality pdb=" CA LEU A 474 " pdb=" N LEU A 474 " pdb=" C LEU A 474 " pdb=" CB LEU A 474 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" CA ALA A 475 " pdb=" N ALA A 475 " pdb=" C ALA A 475 " pdb=" CB ALA A 475 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA ASN A 473 " pdb=" N ASN A 473 " pdb=" C ASN A 473 " pdb=" CB ASN A 473 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 5736 not shown) Planarity restraints: 6200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 117 " -0.024 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C VAL A 117 " 0.085 2.00e-02 2.50e+03 pdb=" O VAL A 117 " -0.033 2.00e-02 2.50e+03 pdb=" N CYS A 118 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 119 " 0.024 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C PRO A 119 " -0.085 2.00e-02 2.50e+03 pdb=" O PRO A 119 " 0.033 2.00e-02 2.50e+03 pdb=" N HIS A 120 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU I 204 " -0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO I 205 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO I 205 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO I 205 " -0.058 5.00e-02 4.00e+02 ... (remaining 6197 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 339 2.55 - 3.14: 28786 3.14 - 3.73: 56452 3.73 - 4.31: 78762 4.31 - 4.90: 130054 Nonbonded interactions: 294393 Sorted by model distance: nonbonded pdb=" O3G ATP A2000 " pdb="MG MG A2001 " model vdw 1.966 2.170 nonbonded pdb=" O3' A R 20 " pdb="MG MG J1501 " model vdw 1.967 2.170 nonbonded pdb=" CB GLU J 211 " pdb=" OP2 DG P 3 " model vdw 2.013 3.440 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.028 2.170 nonbonded pdb=" OD1 ASP G 15 " pdb=" N ILE G 16 " model vdw 2.042 2.520 ... (remaining 294388 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 5 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 135 or (resid 136 and (name N or na \ me CA or name C or name O or name CB )) or resid 137 through 158 or resid 170 th \ rough 232)) selection = (chain 'H' and (resid 5 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 232)) } 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: 1.720 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: 8.070 Check model and map are aligned: 0.560 Set scattering table: 0.360 Process input model: 108.840 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 : 0.010 0.114 36865 Z= 0.675 Angle : 1.022 21.639 50331 Z= 0.584 Chirality : 0.060 0.440 5739 Planarity : 0.006 0.108 6200 Dihedral : 17.096 176.244 14330 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.08 % Favored : 90.68 % Rotamer: Outliers : 0.17 % Allowed : 0.61 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.12), residues: 4294 helix: -0.90 (0.13), residues: 1496 sheet: -1.77 (0.20), residues: 605 loop : -2.15 (0.12), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP J1193 HIS 0.013 0.002 HIS A 948 PHE 0.033 0.003 PHE J 620 TYR 0.036 0.003 TYR G 177 ARG 0.018 0.001 ARG A1007 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 431 time to evaluate : 4.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 LEU cc_start: 0.8551 (mp) cc_final: 0.8320 (tt) REVERT: A 731 GLU cc_start: 0.8544 (pp20) cc_final: 0.8155 (pp20) REVERT: A 937 GLU cc_start: 0.7560 (pt0) cc_final: 0.7175 (pp20) REVERT: A 1078 LEU cc_start: 0.8633 (tt) cc_final: 0.8327 (tt) REVERT: A 1121 PHE cc_start: 0.6479 (p90) cc_final: 0.6060 (p90) REVERT: G 127 GLN cc_start: 0.8113 (pm20) cc_final: 0.7912 (pm20) REVERT: I 210 LEU cc_start: 0.8421 (mm) cc_final: 0.8218 (mm) REVERT: I 477 GLU cc_start: 0.7509 (mm-30) cc_final: 0.6793 (mm-30) REVERT: I 741 MET cc_start: 0.8335 (mmt) cc_final: 0.8130 (mmm) REVERT: I 842 ASP cc_start: 0.7263 (t0) cc_final: 0.6800 (p0) REVERT: I 958 LYS cc_start: 0.9014 (ttmt) cc_final: 0.8810 (ttmm) REVERT: J 267 ASP cc_start: 0.8187 (t0) cc_final: 0.7863 (t0) REVERT: J 304 ASP cc_start: 0.8580 (t0) cc_final: 0.8364 (t0) REVERT: J 1174 ARG cc_start: 0.7589 (mtm-85) cc_final: 0.7226 (mtm-85) REVERT: K 54 ILE cc_start: 0.8935 (mm) cc_final: 0.8701 (mm) REVERT: K 69 ARG cc_start: 0.7824 (mtp-110) cc_final: 0.7333 (ttm-80) outliers start: 6 outliers final: 5 residues processed: 436 average time/residue: 0.4947 time to fit residues: 349.3086 Evaluate side-chains 361 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 356 time to evaluate : 3.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain J residue 710 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 369 optimal weight: 7.9990 chunk 331 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 223 optimal weight: 0.3980 chunk 177 optimal weight: 6.9990 chunk 343 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 208 optimal weight: 0.6980 chunk 255 optimal weight: 9.9990 chunk 397 optimal weight: 9.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS A 159 HIS A 466 ASN A 515 ASN A 539 ASN A 574 GLN ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 HIS H 37 HIS H 227 GLN I 69 GLN I 273 HIS I1061 GLN J 209 ASN ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36865 Z= 0.192 Angle : 0.602 10.902 50331 Z= 0.312 Chirality : 0.042 0.194 5739 Planarity : 0.005 0.075 6200 Dihedral : 15.644 177.233 6001 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.15 % Favored : 93.71 % Rotamer: Outliers : 0.69 % Allowed : 7.36 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.12), residues: 4294 helix: -0.22 (0.13), residues: 1508 sheet: -1.52 (0.21), residues: 574 loop : -2.03 (0.12), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 260 HIS 0.008 0.001 HIS A 918 PHE 0.016 0.001 PHE A 172 TYR 0.019 0.001 TYR G 177 ARG 0.007 0.000 ARG A1140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 436 time to evaluate : 4.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 TYR cc_start: 0.7565 (m-80) cc_final: 0.7096 (m-80) REVERT: A 283 VAL cc_start: 0.9344 (t) cc_final: 0.9049 (m) REVERT: A 413 MET cc_start: 0.7892 (mmp) cc_final: 0.7505 (mmt) REVERT: A 509 LEU cc_start: 0.8513 (mp) cc_final: 0.8293 (tt) REVERT: A 513 TYR cc_start: 0.8513 (m-80) cc_final: 0.8279 (m-80) REVERT: A 731 GLU cc_start: 0.8425 (pp20) cc_final: 0.8092 (pp20) REVERT: A 937 GLU cc_start: 0.7492 (pt0) cc_final: 0.7135 (pp20) REVERT: A 1121 PHE cc_start: 0.6460 (p90) cc_final: 0.6156 (p90) REVERT: I 210 LEU cc_start: 0.8501 (mm) cc_final: 0.8262 (mm) REVERT: I 434 ASP cc_start: 0.7711 (m-30) cc_final: 0.7480 (m-30) REVERT: I 477 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7235 (mm-30) REVERT: I 842 ASP cc_start: 0.7171 (t0) cc_final: 0.6721 (p0) REVERT: I 1066 MET cc_start: 0.8841 (ptp) cc_final: 0.8605 (ptp) REVERT: I 1206 THR cc_start: 0.9226 (t) cc_final: 0.8997 (m) REVERT: J 267 ASP cc_start: 0.8021 (t0) cc_final: 0.7705 (t0) REVERT: J 478 LEU cc_start: 0.9176 (mt) cc_final: 0.8885 (mt) REVERT: J 500 ILE cc_start: 0.9212 (mm) cc_final: 0.8737 (pt) REVERT: J 516 ASP cc_start: 0.8609 (p0) cc_final: 0.8299 (p0) REVERT: J 727 ASP cc_start: 0.8712 (t70) cc_final: 0.8505 (t0) REVERT: J 1174 ARG cc_start: 0.7762 (mtm-85) cc_final: 0.7432 (mtm180) REVERT: J 1206 ARG cc_start: 0.6649 (ptm-80) cc_final: 0.6432 (ptm-80) REVERT: J 1287 ILE cc_start: 0.9173 (pt) cc_final: 0.8949 (mt) REVERT: K 69 ARG cc_start: 0.7977 (mtp-110) cc_final: 0.7671 (ttm-80) outliers start: 25 outliers final: 13 residues processed: 444 average time/residue: 0.5337 time to fit residues: 392.5536 Evaluate side-chains 397 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 384 time to evaluate : 3.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain K residue 4 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 331 optimal weight: 2.9990 chunk 270 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 398 optimal weight: 4.9990 chunk 430 optimal weight: 3.9990 chunk 354 optimal weight: 3.9990 chunk 395 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 319 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 ASN A 539 ASN ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 GLN K 15 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 36865 Z= 0.401 Angle : 0.652 10.281 50331 Z= 0.336 Chirality : 0.045 0.184 5739 Planarity : 0.005 0.064 6200 Dihedral : 15.657 176.187 5993 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.20 % Favored : 91.66 % Rotamer: Outliers : 1.74 % Allowed : 10.89 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.12), residues: 4294 helix: 0.02 (0.13), residues: 1494 sheet: -1.47 (0.21), residues: 570 loop : -2.03 (0.12), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 260 HIS 0.008 0.001 HIS A 918 PHE 0.017 0.002 PHE J 620 TYR 0.022 0.002 TYR G 177 ARG 0.005 0.000 ARG I1034 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 394 time to evaluate : 3.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 TYR cc_start: 0.8526 (m-80) cc_final: 0.7984 (m-80) REVERT: A 731 GLU cc_start: 0.8553 (pp20) cc_final: 0.8216 (pp20) REVERT: A 847 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7434 (pm20) REVERT: A 927 GLN cc_start: 0.8078 (mt0) cc_final: 0.7428 (mp10) REVERT: A 937 GLU cc_start: 0.7602 (pt0) cc_final: 0.7172 (pp20) REVERT: A 1067 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6786 (mmm-85) REVERT: A 1121 PHE cc_start: 0.6481 (p90) cc_final: 0.6180 (p90) REVERT: I 210 LEU cc_start: 0.8514 (mm) cc_final: 0.8298 (mm) REVERT: I 434 ASP cc_start: 0.7656 (m-30) cc_final: 0.7449 (m-30) REVERT: I 542 ARG cc_start: 0.8268 (mmt180) cc_final: 0.7999 (mtp180) REVERT: I 842 ASP cc_start: 0.7242 (t0) cc_final: 0.6741 (p0) REVERT: J 267 ASP cc_start: 0.8177 (t0) cc_final: 0.7814 (t0) REVERT: J 478 LEU cc_start: 0.9134 (mt) cc_final: 0.8836 (mt) REVERT: J 516 ASP cc_start: 0.8681 (p0) cc_final: 0.8331 (p0) REVERT: J 1174 ARG cc_start: 0.7682 (mtm-85) cc_final: 0.7363 (mtm-85) REVERT: J 1287 ILE cc_start: 0.9160 (pt) cc_final: 0.8926 (mt) REVERT: K 69 ARG cc_start: 0.7980 (mtp-110) cc_final: 0.7739 (ttm-80) outliers start: 63 outliers final: 38 residues processed: 432 average time/residue: 0.4646 time to fit residues: 332.2069 Evaluate side-chains 411 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 371 time to evaluate : 3.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1067 ARG Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 15 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 8.9990 chunk 299 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 190 optimal weight: 7.9990 chunk 267 optimal weight: 2.9990 chunk 399 optimal weight: 9.9990 chunk 423 optimal weight: 7.9990 chunk 208 optimal weight: 0.9980 chunk 379 optimal weight: 0.3980 chunk 114 optimal weight: 0.0070 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 ASN A 539 ASN ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 965 GLN J 424 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36865 Z= 0.189 Angle : 0.566 11.081 50331 Z= 0.291 Chirality : 0.042 0.176 5739 Planarity : 0.004 0.060 6200 Dihedral : 15.488 177.429 5993 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.31 % Favored : 93.57 % Rotamer: Outliers : 1.46 % Allowed : 13.02 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.13), residues: 4294 helix: 0.33 (0.14), residues: 1503 sheet: -1.32 (0.21), residues: 567 loop : -1.94 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 260 HIS 0.008 0.001 HIS A 918 PHE 0.014 0.001 PHE A 195 TYR 0.018 0.001 TYR H 177 ARG 0.005 0.000 ARG I1034 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 410 time to evaluate : 4.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 GLU cc_start: 0.8455 (pp20) cc_final: 0.8238 (pp20) REVERT: A 847 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7310 (pm20) REVERT: A 927 GLN cc_start: 0.8052 (mt0) cc_final: 0.7602 (mp10) REVERT: A 937 GLU cc_start: 0.7608 (pt0) cc_final: 0.7196 (pp20) REVERT: A 963 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7741 (mt0) REVERT: A 1121 PHE cc_start: 0.6643 (p90) cc_final: 0.6318 (p90) REVERT: I 210 LEU cc_start: 0.8547 (mm) cc_final: 0.8324 (mm) REVERT: I 542 ARG cc_start: 0.8318 (mmt180) cc_final: 0.8022 (mtp180) REVERT: I 842 ASP cc_start: 0.7192 (t0) cc_final: 0.6688 (p0) REVERT: I 954 LYS cc_start: 0.9007 (ttmm) cc_final: 0.8794 (mtpt) REVERT: I 1174 GLU cc_start: 0.8282 (tp30) cc_final: 0.7923 (tp30) REVERT: I 1180 MET cc_start: 0.8924 (ttt) cc_final: 0.8684 (ttm) REVERT: J 183 GLU cc_start: 0.8015 (tp30) cc_final: 0.7789 (tp30) REVERT: J 188 LEU cc_start: 0.8707 (tt) cc_final: 0.8423 (tt) REVERT: J 267 ASP cc_start: 0.8113 (t0) cc_final: 0.7720 (t0) REVERT: J 478 LEU cc_start: 0.9120 (mt) cc_final: 0.8801 (mt) REVERT: J 500 ILE cc_start: 0.9216 (mm) cc_final: 0.8831 (pt) REVERT: J 516 ASP cc_start: 0.8659 (p0) cc_final: 0.8295 (p0) REVERT: J 1174 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7430 (mtm-85) REVERT: J 1305 ASP cc_start: 0.8370 (m-30) cc_final: 0.7887 (m-30) REVERT: K 69 ARG cc_start: 0.7871 (mtp-110) cc_final: 0.7645 (ttm-80) outliers start: 53 outliers final: 32 residues processed: 444 average time/residue: 0.4734 time to fit residues: 350.4831 Evaluate side-chains 420 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 386 time to evaluate : 4.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain K residue 11 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 5.9990 chunk 240 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 315 optimal weight: 0.0570 chunk 174 optimal weight: 8.9990 chunk 361 optimal weight: 5.9990 chunk 292 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 216 optimal weight: 6.9990 chunk 380 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 overall best weight: 3.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 ASN A 539 ASN A 664 GLN A 859 HIS H 227 GLN ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 36865 Z= 0.417 Angle : 0.640 9.882 50331 Z= 0.329 Chirality : 0.045 0.215 5739 Planarity : 0.004 0.059 6200 Dihedral : 15.553 176.143 5993 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.43 % Favored : 91.45 % Rotamer: Outliers : 2.15 % Allowed : 14.04 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.13), residues: 4294 helix: 0.33 (0.14), residues: 1498 sheet: -1.38 (0.21), residues: 580 loop : -1.90 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 260 HIS 0.008 0.001 HIS A 918 PHE 0.016 0.002 PHE J 620 TYR 0.020 0.002 TYR G 177 ARG 0.007 0.000 ARG I1211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 387 time to evaluate : 4.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8754 (tt) REVERT: A 518 LYS cc_start: 0.8688 (mttp) cc_final: 0.8363 (mtpp) REVERT: A 731 GLU cc_start: 0.8594 (pp20) cc_final: 0.8310 (pp20) REVERT: A 847 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7333 (pm20) REVERT: A 927 GLN cc_start: 0.8017 (mt0) cc_final: 0.7567 (mp10) REVERT: A 937 GLU cc_start: 0.7638 (pt0) cc_final: 0.7250 (pp20) REVERT: A 938 ASP cc_start: 0.8305 (m-30) cc_final: 0.8069 (m-30) REVERT: A 963 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7782 (mt0) REVERT: A 1121 PHE cc_start: 0.6691 (p90) cc_final: 0.6374 (p90) REVERT: H 181 GLU cc_start: 0.7822 (mp0) cc_final: 0.7493 (mp0) REVERT: I 126 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7862 (tp30) REVERT: I 239 MET cc_start: 0.3516 (ttp) cc_final: 0.3113 (ttp) REVERT: I 542 ARG cc_start: 0.8369 (mmt180) cc_final: 0.8029 (mtp180) REVERT: I 842 ASP cc_start: 0.7266 (t0) cc_final: 0.6724 (p0) REVERT: I 954 LYS cc_start: 0.8989 (ttmm) cc_final: 0.8764 (mtpt) REVERT: J 47 ARG cc_start: 0.7923 (ptp-110) cc_final: 0.7696 (ptp-110) REVERT: J 188 LEU cc_start: 0.8760 (tt) cc_final: 0.8489 (tt) REVERT: J 267 ASP cc_start: 0.8192 (t0) cc_final: 0.7808 (t0) REVERT: J 478 LEU cc_start: 0.9129 (mt) cc_final: 0.8804 (mt) REVERT: J 516 ASP cc_start: 0.8717 (p0) cc_final: 0.8369 (p0) REVERT: J 712 GLN cc_start: 0.8382 (pp30) cc_final: 0.8036 (pp30) REVERT: J 1174 ARG cc_start: 0.7540 (mtm-85) cc_final: 0.7297 (mtm-85) REVERT: J 1275 LEU cc_start: 0.8499 (tp) cc_final: 0.8227 (tt) REVERT: J 1305 ASP cc_start: 0.8422 (m-30) cc_final: 0.7951 (m-30) REVERT: K 69 ARG cc_start: 0.7909 (mtp-110) cc_final: 0.7661 (ttm-80) outliers start: 78 outliers final: 54 residues processed: 440 average time/residue: 0.4649 time to fit residues: 338.8632 Evaluate side-chains 428 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 371 time to evaluate : 4.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 741 ARG Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain K residue 11 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 20.0000 chunk 381 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 423 optimal weight: 0.9990 chunk 351 optimal weight: 5.9990 chunk 196 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 222 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 ASN A 539 ASN G 147 GLN ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 36865 Z= 0.324 Angle : 0.606 11.822 50331 Z= 0.311 Chirality : 0.043 0.247 5739 Planarity : 0.004 0.065 6200 Dihedral : 15.506 176.548 5993 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.50 % Favored : 92.38 % Rotamer: Outliers : 2.34 % Allowed : 15.36 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.13), residues: 4294 helix: 0.42 (0.14), residues: 1496 sheet: -1.41 (0.21), residues: 574 loop : -1.86 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 260 HIS 0.008 0.001 HIS I 273 PHE 0.015 0.001 PHE A 643 TYR 0.021 0.001 TYR H 177 ARG 0.006 0.000 ARG I1034 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 387 time to evaluate : 3.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8758 (tt) REVERT: A 731 GLU cc_start: 0.8519 (pp20) cc_final: 0.8306 (pp20) REVERT: A 847 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7284 (pm20) REVERT: A 927 GLN cc_start: 0.8022 (mt0) cc_final: 0.7515 (mp10) REVERT: A 937 GLU cc_start: 0.7484 (pt0) cc_final: 0.7176 (pp20) REVERT: A 963 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7778 (mt0) REVERT: A 1121 PHE cc_start: 0.6668 (p90) cc_final: 0.6349 (p90) REVERT: H 181 GLU cc_start: 0.7818 (mp0) cc_final: 0.7473 (mp0) REVERT: I 126 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7858 (tp30) REVERT: I 542 ARG cc_start: 0.8393 (mmt180) cc_final: 0.8012 (mmt180) REVERT: I 842 ASP cc_start: 0.7252 (t0) cc_final: 0.6614 (p0) REVERT: I 954 LYS cc_start: 0.9072 (ttmm) cc_final: 0.8808 (mtpt) REVERT: I 994 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6954 (ttm170) REVERT: I 1034 ARG cc_start: 0.8384 (mtp-110) cc_final: 0.8131 (mtp85) REVERT: I 1174 GLU cc_start: 0.8259 (tp30) cc_final: 0.7905 (tp30) REVERT: J 188 LEU cc_start: 0.8737 (tt) cc_final: 0.8452 (tt) REVERT: J 267 ASP cc_start: 0.8179 (t0) cc_final: 0.7776 (t0) REVERT: J 478 LEU cc_start: 0.9121 (mt) cc_final: 0.8797 (mt) REVERT: J 516 ASP cc_start: 0.8711 (p0) cc_final: 0.8360 (p0) REVERT: J 1174 ARG cc_start: 0.7498 (mtm-85) cc_final: 0.7233 (mtm-85) REVERT: J 1305 ASP cc_start: 0.8427 (m-30) cc_final: 0.8205 (m-30) REVERT: K 69 ARG cc_start: 0.7890 (mtp-110) cc_final: 0.7664 (ttm-80) outliers start: 85 outliers final: 68 residues processed: 440 average time/residue: 0.4597 time to fit residues: 335.1942 Evaluate side-chains 449 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 377 time to evaluate : 3.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 994 ARG Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain K residue 11 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 241 optimal weight: 5.9990 chunk 309 optimal weight: 2.9990 chunk 239 optimal weight: 0.6980 chunk 356 optimal weight: 0.8980 chunk 236 optimal weight: 0.8980 chunk 422 optimal weight: 4.9990 chunk 264 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 chunk 194 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 ASN A 539 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 ASN J 465 GLN J 792 ASN K 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36865 Z= 0.164 Angle : 0.545 11.852 50331 Z= 0.280 Chirality : 0.041 0.214 5739 Planarity : 0.004 0.062 6200 Dihedral : 15.306 177.194 5993 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.40 % Favored : 93.53 % Rotamer: Outliers : 2.01 % Allowed : 16.11 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.13), residues: 4294 helix: 0.72 (0.14), residues: 1501 sheet: -1.21 (0.22), residues: 567 loop : -1.78 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 260 HIS 0.006 0.001 HIS A 918 PHE 0.013 0.001 PHE A 195 TYR 0.022 0.001 TYR H 177 ARG 0.007 0.000 ARG I1034 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 415 time to evaluate : 3.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 847 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7504 (pm20) REVERT: A 937 GLU cc_start: 0.7348 (pt0) cc_final: 0.7052 (pp20) REVERT: A 959 LEU cc_start: 0.9534 (tp) cc_final: 0.9228 (tp) REVERT: A 963 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7680 (mt0) REVERT: A 1121 PHE cc_start: 0.6588 (p90) cc_final: 0.6285 (p90) REVERT: I 126 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7805 (tp30) REVERT: I 445 ILE cc_start: 0.8971 (pt) cc_final: 0.8756 (pt) REVERT: I 472 GLU cc_start: 0.8374 (pp20) cc_final: 0.7870 (pt0) REVERT: I 542 ARG cc_start: 0.8439 (mmt180) cc_final: 0.8060 (mtp180) REVERT: I 954 LYS cc_start: 0.9041 (ttmm) cc_final: 0.8796 (mtpt) REVERT: I 1178 LYS cc_start: 0.9274 (mtmt) cc_final: 0.9068 (mtpp) REVERT: J 183 GLU cc_start: 0.8146 (tp30) cc_final: 0.7801 (tp30) REVERT: J 188 LEU cc_start: 0.8600 (tt) cc_final: 0.8284 (tt) REVERT: J 267 ASP cc_start: 0.8115 (t0) cc_final: 0.7684 (t0) REVERT: J 478 LEU cc_start: 0.9088 (mt) cc_final: 0.8747 (mt) REVERT: J 500 ILE cc_start: 0.9287 (mm) cc_final: 0.8829 (pt) REVERT: J 516 ASP cc_start: 0.8654 (p0) cc_final: 0.8295 (p0) REVERT: J 712 GLN cc_start: 0.8339 (pp30) cc_final: 0.7774 (pp30) REVERT: J 1174 ARG cc_start: 0.7582 (mtm-85) cc_final: 0.7282 (mtm-85) REVERT: K 69 ARG cc_start: 0.7864 (mtp-110) cc_final: 0.7606 (ttm-80) outliers start: 73 outliers final: 49 residues processed: 463 average time/residue: 0.4611 time to fit residues: 352.0130 Evaluate side-chains 434 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 383 time to evaluate : 3.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain K residue 11 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 chunk 252 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 268 optimal weight: 7.9990 chunk 287 optimal weight: 0.6980 chunk 208 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 331 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 ASN A 539 ASN H 147 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 36865 Z= 0.258 Angle : 0.576 11.485 50331 Z= 0.295 Chirality : 0.042 0.209 5739 Planarity : 0.004 0.062 6200 Dihedral : 15.300 176.389 5993 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.08 % Favored : 92.83 % Rotamer: Outliers : 2.01 % Allowed : 16.63 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.13), residues: 4294 helix: 0.77 (0.14), residues: 1497 sheet: -1.23 (0.21), residues: 583 loop : -1.74 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J1193 HIS 0.007 0.001 HIS A 918 PHE 0.041 0.001 PHE I 828 TYR 0.021 0.001 TYR H 177 ARG 0.007 0.000 ARG I1034 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 381 time to evaluate : 3.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 847 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7351 (pm20) REVERT: A 927 GLN cc_start: 0.7988 (mt0) cc_final: 0.7529 (mp10) REVERT: A 937 GLU cc_start: 0.7364 (pt0) cc_final: 0.7071 (pp20) REVERT: A 1121 PHE cc_start: 0.6610 (p90) cc_final: 0.6307 (p90) REVERT: I 126 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7847 (tp30) REVERT: I 359 ARG cc_start: 0.7017 (ptm-80) cc_final: 0.6670 (ptm-80) REVERT: I 445 ILE cc_start: 0.8982 (pt) cc_final: 0.8767 (pt) REVERT: I 472 GLU cc_start: 0.8400 (pp20) cc_final: 0.7898 (pt0) REVERT: I 542 ARG cc_start: 0.8421 (mmt180) cc_final: 0.8068 (mtp180) REVERT: I 1034 ARG cc_start: 0.8387 (mtp-110) cc_final: 0.8120 (mtp85) REVERT: J 47 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7579 (ptp-170) REVERT: J 183 GLU cc_start: 0.8157 (tp30) cc_final: 0.7803 (tp30) REVERT: J 188 LEU cc_start: 0.8602 (tt) cc_final: 0.8291 (tt) REVERT: J 213 LYS cc_start: 0.7978 (mttm) cc_final: 0.7629 (mtpt) REVERT: J 267 ASP cc_start: 0.8190 (t0) cc_final: 0.7756 (t0) REVERT: J 478 LEU cc_start: 0.9081 (mt) cc_final: 0.8733 (mt) REVERT: J 500 ILE cc_start: 0.9279 (mm) cc_final: 0.8841 (pt) REVERT: J 516 ASP cc_start: 0.8690 (p0) cc_final: 0.8319 (p0) REVERT: J 1174 ARG cc_start: 0.7569 (mtm-85) cc_final: 0.7241 (mtm-85) REVERT: K 69 ARG cc_start: 0.7888 (mtp-110) cc_final: 0.7646 (ttm-80) outliers start: 73 outliers final: 59 residues processed: 428 average time/residue: 0.4812 time to fit residues: 342.5132 Evaluate side-chains 435 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 374 time to evaluate : 3.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 854 ILE Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain K residue 11 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 10.0000 chunk 404 optimal weight: 3.9990 chunk 368 optimal weight: 5.9990 chunk 393 optimal weight: 0.0040 chunk 236 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 chunk 308 optimal weight: 8.9990 chunk 120 optimal weight: 0.8980 chunk 355 optimal weight: 3.9990 chunk 372 optimal weight: 0.8980 chunk 392 optimal weight: 6.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 ASN A 539 ASN ** A1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1069 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS J 489 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36865 Z= 0.164 Angle : 0.549 11.691 50331 Z= 0.280 Chirality : 0.041 0.208 5739 Planarity : 0.004 0.060 6200 Dihedral : 15.196 176.517 5993 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.83 % Rotamer: Outliers : 1.79 % Allowed : 17.18 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.13), residues: 4294 helix: 0.91 (0.14), residues: 1508 sheet: -1.09 (0.21), residues: 585 loop : -1.66 (0.13), residues: 2201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1134 HIS 0.007 0.001 HIS A 918 PHE 0.030 0.001 PHE I 828 TYR 0.026 0.001 TYR H 177 ARG 0.007 0.000 ARG I1034 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 405 time to evaluate : 4.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 847 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7353 (pm20) REVERT: A 937 GLU cc_start: 0.7150 (pt0) cc_final: 0.6925 (pp20) REVERT: A 959 LEU cc_start: 0.9520 (tp) cc_final: 0.9287 (tp) REVERT: A 1121 PHE cc_start: 0.6543 (p90) cc_final: 0.6325 (p90) REVERT: I 359 ARG cc_start: 0.6946 (ptm-80) cc_final: 0.6650 (ptm-80) REVERT: I 445 ILE cc_start: 0.8963 (pt) cc_final: 0.8745 (pt) REVERT: I 472 GLU cc_start: 0.8391 (pp20) cc_final: 0.7881 (pt0) REVERT: I 542 ARG cc_start: 0.8425 (mmt180) cc_final: 0.8043 (mtp180) REVERT: I 1034 ARG cc_start: 0.8347 (mtp-110) cc_final: 0.8085 (mtp85) REVERT: I 1178 LYS cc_start: 0.9305 (mtmt) cc_final: 0.9073 (mtpp) REVERT: J 47 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7618 (ptp-170) REVERT: J 183 GLU cc_start: 0.8123 (tp30) cc_final: 0.7771 (tp30) REVERT: J 188 LEU cc_start: 0.8592 (tt) cc_final: 0.8120 (tt) REVERT: J 267 ASP cc_start: 0.8121 (t0) cc_final: 0.7701 (t0) REVERT: J 478 LEU cc_start: 0.9075 (mt) cc_final: 0.8720 (mt) REVERT: J 500 ILE cc_start: 0.9263 (mm) cc_final: 0.8838 (pt) REVERT: J 516 ASP cc_start: 0.8631 (p0) cc_final: 0.8258 (p0) REVERT: J 532 GLU cc_start: 0.7976 (tt0) cc_final: 0.7675 (tt0) REVERT: J 712 GLN cc_start: 0.8342 (pp30) cc_final: 0.7753 (pp30) REVERT: J 1174 ARG cc_start: 0.7540 (mtm-85) cc_final: 0.7156 (mtm-85) REVERT: K 69 ARG cc_start: 0.7856 (mtp-110) cc_final: 0.7645 (ttm-80) REVERT: K 72 GLN cc_start: 0.7228 (pp30) cc_final: 0.6994 (pp30) outliers start: 65 outliers final: 52 residues processed: 442 average time/residue: 0.4664 time to fit residues: 348.3690 Evaluate side-chains 439 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 385 time to evaluate : 3.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 854 ILE Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain K residue 11 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 10.0000 chunk 415 optimal weight: 5.9990 chunk 253 optimal weight: 8.9990 chunk 197 optimal weight: 0.9980 chunk 289 optimal weight: 0.0000 chunk 436 optimal weight: 4.9990 chunk 401 optimal weight: 0.4980 chunk 347 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 268 optimal weight: 6.9990 chunk 213 optimal weight: 0.4980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 ASN A 539 ASN I 139 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 922 ASN I1220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 36865 Z= 0.155 Angle : 0.547 11.659 50331 Z= 0.278 Chirality : 0.041 0.251 5739 Planarity : 0.004 0.058 6200 Dihedral : 15.104 175.985 5993 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.17 % Favored : 93.78 % Rotamer: Outliers : 1.65 % Allowed : 17.29 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.13), residues: 4294 helix: 1.04 (0.14), residues: 1510 sheet: -0.93 (0.22), residues: 562 loop : -1.56 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A1134 HIS 0.006 0.001 HIS A 918 PHE 0.026 0.001 PHE I1221 TYR 0.018 0.001 TYR J 679 ARG 0.009 0.000 ARG G 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 408 time to evaluate : 4.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 PHE cc_start: 0.5385 (t80) cc_final: 0.4987 (t80) REVERT: A 847 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7072 (pm20) REVERT: A 927 GLN cc_start: 0.7849 (mt0) cc_final: 0.7516 (mp10) REVERT: A 1121 PHE cc_start: 0.6637 (p90) cc_final: 0.6335 (p90) REVERT: I 359 ARG cc_start: 0.7020 (ptm-80) cc_final: 0.6750 (ptm-80) REVERT: I 403 MET cc_start: 0.8810 (tmm) cc_final: 0.8600 (ttp) REVERT: I 445 ILE cc_start: 0.8941 (pt) cc_final: 0.8704 (pt) REVERT: I 472 GLU cc_start: 0.8396 (pp20) cc_final: 0.7890 (pt0) REVERT: I 542 ARG cc_start: 0.8414 (mmt180) cc_final: 0.8028 (mtp180) REVERT: I 800 MET cc_start: 0.8343 (ptp) cc_final: 0.8114 (mtm) REVERT: I 1034 ARG cc_start: 0.8346 (mtp-110) cc_final: 0.8066 (mtp85) REVERT: J 183 GLU cc_start: 0.8126 (tp30) cc_final: 0.7768 (tp30) REVERT: J 267 ASP cc_start: 0.8111 (t0) cc_final: 0.7712 (t0) REVERT: J 478 LEU cc_start: 0.9074 (mt) cc_final: 0.8728 (mt) REVERT: J 500 ILE cc_start: 0.9281 (mm) cc_final: 0.8897 (pt) REVERT: J 516 ASP cc_start: 0.8602 (p0) cc_final: 0.8232 (p0) REVERT: J 712 GLN cc_start: 0.8357 (pp30) cc_final: 0.7738 (pp30) REVERT: J 1174 ARG cc_start: 0.7544 (mtm-85) cc_final: 0.7185 (mtm-85) REVERT: K 72 GLN cc_start: 0.7193 (pp30) cc_final: 0.6977 (pp30) outliers start: 60 outliers final: 53 residues processed: 447 average time/residue: 0.4664 time to fit residues: 352.3660 Evaluate side-chains 434 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 380 time to evaluate : 3.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 854 ILE Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain K residue 11 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 0.7980 chunk 370 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 320 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 348 optimal weight: 0.8980 chunk 145 optimal weight: 10.0000 chunk 357 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 ASN H 132 HIS ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 834 GLN I 922 ASN J 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.135349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.099948 restraints weight = 59223.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.100784 restraints weight = 45024.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.100943 restraints weight = 33016.118| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36865 Z= 0.178 Angle : 0.557 11.570 50331 Z= 0.283 Chirality : 0.041 0.200 5739 Planarity : 0.004 0.058 6200 Dihedral : 15.088 175.352 5993 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.15 % Favored : 93.81 % Rotamer: Outliers : 1.82 % Allowed : 17.73 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 4294 helix: 1.07 (0.14), residues: 1505 sheet: -0.86 (0.22), residues: 561 loop : -1.54 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A1134 HIS 0.007 0.001 HIS A 918 PHE 0.026 0.001 PHE I 337 TYR 0.026 0.001 TYR H 177 ARG 0.007 0.000 ARG I1034 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7196.51 seconds wall clock time: 131 minutes 32.20 seconds (7892.20 seconds total)