Starting phenix.real_space_refine on Sat Dec 9 16:01:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh6_12895/12_2023/7oh6_12895_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh6_12895/12_2023/7oh6_12895.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh6_12895/12_2023/7oh6_12895_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh6_12895/12_2023/7oh6_12895_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh6_12895/12_2023/7oh6_12895_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh6_12895/12_2023/7oh6_12895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh6_12895/12_2023/7oh6_12895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh6_12895/12_2023/7oh6_12895_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh6_12895/12_2023/7oh6_12895_updated.pdb" } resolution = 3.0 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= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 3 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 7470 2.51 5 N 1858 2.21 5 O 2167 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 309": "NH1" <-> "NH2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 730": "NH1" <-> "NH2" Residue "A ARG 744": "NH1" <-> "NH2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A ARG 850": "NH1" <-> "NH2" Residue "A ARG 866": "NH1" <-> "NH2" Residue "A ARG 871": "NH1" <-> "NH2" Residue "A ARG 928": "NH1" <-> "NH2" Residue "A ARG 943": "NH1" <-> "NH2" Residue "A ARG 1071": "NH1" <-> "NH2" Residue "A PHE 1215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1219": "NH1" <-> "NH2" Residue "C ARG 112": "NH1" <-> "NH2" Residue "C TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 359": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11552 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8504 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 30, 'TRANS': 1033} Chain: "C" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2842 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 21, 'TRANS': 328} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 123 Unusual residues: {' MG': 1, '2Y5': 1, 'ALF': 1, 'Q3G': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 6.22, per 1000 atoms: 0.54 Number of scatterers: 11552 At special positions: 0 Unit cell: (73.2152, 106.214, 174.273, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 48 16.00 P 3 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 2167 8.00 N 1858 7.00 C 7470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 123 " distance=2.06 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 190 " distance=2.14 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG B 1 " - " ASN C 288 " " NAG C 501 " - " ASN C 216 " " NAG D 1 " - " ASN C 199 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.27 Conformation dependent library (CDL) restraints added in 2.2 seconds 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2676 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 10 sheets defined 40.2% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 190 through 196 removed outlier: 4.816A pdb=" N SER A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N PHE A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 removed outlier: 4.125A pdb=" N PHE A 219 " --> pdb=" O PRO A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 249 through 280 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 439 through 472 removed outlier: 3.848A pdb=" N ARG A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 488 through 505 removed outlier: 4.202A pdb=" N LYS A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASN A 504 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 527 removed outlier: 4.178A pdb=" N GLU A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 545 through 552 removed outlier: 5.396A pdb=" N GLU A 549 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY A 552 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 618 through 632 Proline residue: A 621 - end of helix removed outlier: 3.836A pdb=" N ASN A 624 " --> pdb=" O PRO A 621 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR A 632 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 removed outlier: 3.507A pdb=" N LEU A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 730 removed outlier: 5.512A pdb=" N GLU A 729 " --> pdb=" O THR A 725 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG A 730 " --> pdb=" O VAL A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 750 Processing helix chain 'A' and resid 766 through 781 removed outlier: 3.655A pdb=" N SER A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 839 through 848 Processing helix chain 'A' and resid 866 through 882 removed outlier: 3.554A pdb=" N GLU A 882 " --> pdb=" O ASN A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 Processing helix chain 'A' and resid 899 through 905 removed outlier: 4.071A pdb=" N PHE A 904 " --> pdb=" O LYS A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 918 Processing helix chain 'A' and resid 931 through 943 removed outlier: 3.892A pdb=" N ALA A 935 " --> pdb=" O PRO A 931 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 938 " --> pdb=" O LYS A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 964 Processing helix chain 'A' and resid 978 through 982 Processing helix chain 'A' and resid 990 through 1016 removed outlier: 3.936A pdb=" N LYS A 994 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 996 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU A 998 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N VAL A 999 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N HIS A1000 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY A1001 " --> pdb=" O LEU A 998 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TRP A1003 " --> pdb=" O HIS A1000 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER A1004 " --> pdb=" O GLY A1001 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE A1008 " --> pdb=" O TYR A1005 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER A1009 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR A1014 " --> pdb=" O ALA A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1023 No H-bonds generated for 'chain 'A' and resid 1020 through 1023' Processing helix chain 'A' and resid 1025 through 1028 No H-bonds generated for 'chain 'A' and resid 1025 through 1028' Processing helix chain 'A' and resid 1043 through 1052 removed outlier: 4.505A pdb=" N ASN A1050 " --> pdb=" O MET A1046 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1062 Processing helix chain 'A' and resid 1070 through 1075 Processing helix chain 'A' and resid 1077 through 1084 Processing helix chain 'A' and resid 1091 through 1115 Processing helix chain 'A' and resid 1132 through 1153 removed outlier: 4.078A pdb=" N THR A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1179 Proline residue: A1177 - end of helix Processing helix chain 'A' and resid 1195 through 1200 Processing helix chain 'A' and resid 1203 through 1230 Proline residue: A1213 - end of helix removed outlier: 5.055A pdb=" N ARG A1219 " --> pdb=" O PHE A1215 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASP A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1244 removed outlier: 3.536A pdb=" N TYR A1244 " --> pdb=" O GLU A1240 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 68 removed outlier: 3.852A pdb=" N LEU C 46 " --> pdb=" O PRO C 42 " (cutoff:3.500A) Proline residue: C 47 - end of helix removed outlier: 3.783A pdb=" N THR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) Proline residue: C 58 - end of helix Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 151 through 154 No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 174 through 179 Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 191 through 195 removed outlier: 3.715A pdb=" N ASN C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 191 through 195' Processing helix chain 'C' and resid 227 through 230 No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 245 through 247 No H-bonds generated for 'chain 'C' and resid 245 through 247' Processing helix chain 'C' and resid 267 through 273 Processing helix chain 'C' and resid 308 through 310 No H-bonds generated for 'chain 'C' and resid 308 through 310' Processing helix chain 'C' and resid 331 through 356 Processing sheet with id= A, first strand: chain 'A' and resid 183 through 186 Processing sheet with id= B, first strand: chain 'A' and resid 286 through 288 Processing sheet with id= C, first strand: chain 'A' and resid 307 through 310 removed outlier: 6.988A pdb=" N ASP A 319 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 346 through 348 removed outlier: 3.881A pdb=" N TYR A 333 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 985 through 987 removed outlier: 6.258A pdb=" N TYR A 556 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE A 952 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE A 558 " --> pdb=" O ILE A 952 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS A 830 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N SER A 559 " --> pdb=" O LYS A 830 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TRP A 832 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL A 924 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 923 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ASN A 857 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL A 896 " --> pdb=" O ASN A 857 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU A 859 " --> pdb=" O VAL A 896 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ASP A 898 " --> pdb=" O LEU A 859 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE A 861 " --> pdb=" O ASP A 898 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 637 through 639 Processing sheet with id= G, first strand: chain 'A' and resid 687 through 690 removed outlier: 3.699A pdb=" N LYS A 673 " --> pdb=" O SER A 676 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR A 678 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE A 671 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU A 680 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N PHE A 669 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 570 through 577 removed outlier: 6.940A pdb=" N ALA A 808 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N CYS A 575 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA A 806 " --> pdb=" O CYS A 575 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE A 577 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N ILE A 804 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU A 759 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA A 806 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 757 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA A 808 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG A 755 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE A 716 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG A 710 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LEU A 692 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 97 through 100 removed outlier: 6.383A pdb=" N TYR C 141 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU C 284 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE C 143 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N TYR C 282 " --> pdb=" O ILE C 143 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 110 through 115 removed outlier: 4.497A pdb=" N LYS C 297 " --> pdb=" O ILE C 209 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 4.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1862 1.31 - 1.44: 3208 1.44 - 1.56: 6655 1.56 - 1.69: 5 1.69 - 1.82: 81 Bond restraints: 11811 Sorted by residual: bond pdb=" F2 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.685 1.806 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" F3 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.685 1.791 -0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" F4 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.686 1.790 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.684 1.778 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C35 2Y5 A1501 " pdb=" C36 2Y5 A1501 " ideal model delta sigma weight residual 1.568 1.527 0.041 2.00e-02 2.50e+03 4.12e+00 ... (remaining 11806 not shown) Histogram of bond angle deviations from ideal: 89.28 - 107.34: 358 107.34 - 125.39: 15470 125.39 - 143.44: 171 143.44 - 161.49: 0 161.49 - 179.54: 2 Bond angle restraints: 16001 Sorted by residual: angle pdb=" F3 ALF A1502 " pdb="AL ALF A1502 " pdb=" F4 ALF A1502 " ideal model delta sigma weight residual 109.63 179.54 -69.91 3.00e+00 1.11e-01 5.43e+02 angle pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " pdb=" F2 ALF A1502 " ideal model delta sigma weight residual 108.68 177.97 -69.29 3.00e+00 1.11e-01 5.34e+02 angle pdb=" C21 2Y5 A1501 " pdb=" C22 2Y5 A1501 " pdb=" C23 2Y5 A1501 " ideal model delta sigma weight residual 85.82 120.32 -34.50 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C24 2Y5 A1501 " pdb=" C25 2Y5 A1501 " pdb=" C26 2Y5 A1501 " ideal model delta sigma weight residual 152.70 119.65 33.05 3.00e+00 1.11e-01 1.21e+02 angle pdb=" C18 2Y5 A1501 " pdb=" C19 2Y5 A1501 " pdb=" C20 2Y5 A1501 " ideal model delta sigma weight residual 152.65 120.77 31.88 3.00e+00 1.11e-01 1.13e+02 ... (remaining 15996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.49: 6985 32.49 - 64.98: 107 64.98 - 97.47: 7 97.47 - 129.96: 1 129.96 - 162.45: 3 Dihedral angle restraints: 7103 sinusoidal: 2953 harmonic: 4150 Sorted by residual: dihedral pdb=" CA ILE A 670 " pdb=" C ILE A 670 " pdb=" N ILE A 671 " pdb=" CA ILE A 671 " ideal model delta harmonic sigma weight residual 180.00 -155.90 -24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" C24 2Y5 A1501 " pdb=" C25 2Y5 A1501 " pdb=" C26 2Y5 A1501 " pdb=" C27 2Y5 A1501 " ideal model delta sinusoidal sigma weight residual 329.24 166.79 162.45 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C1 2Y5 A1501 " pdb=" O1 2Y5 A1501 " pdb=" P1 2Y5 A1501 " pdb=" O13 2Y5 A1501 " ideal model delta sinusoidal sigma weight residual 64.28 -150.43 -145.29 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 7100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1520 0.055 - 0.109: 259 0.109 - 0.164: 41 0.164 - 0.219: 1 0.219 - 0.273: 1 Chirality restraints: 1822 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CG LEU A 693 " pdb=" CB LEU A 693 " pdb=" CD1 LEU A 693 " pdb=" CD2 LEU A 693 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CA ILE C 92 " pdb=" N ILE C 92 " pdb=" C ILE C 92 " pdb=" CB ILE C 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 1819 not shown) Planarity restraints: 1999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 746 " 0.018 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C LEU A 746 " -0.060 2.00e-02 2.50e+03 pdb=" O LEU A 746 " 0.023 2.00e-02 2.50e+03 pdb=" N GLU A 747 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 621 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C PRO A 621 " 0.056 2.00e-02 2.50e+03 pdb=" O PRO A 621 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE A 622 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 745 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.25e+00 pdb=" C HIS A 745 " -0.053 2.00e-02 2.50e+03 pdb=" O HIS A 745 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU A 746 " 0.018 2.00e-02 2.50e+03 ... (remaining 1996 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 26 2.36 - 2.99: 6060 2.99 - 3.63: 16245 3.63 - 4.26: 25907 4.26 - 4.90: 43751 Nonbonded interactions: 91989 Sorted by model distance: nonbonded pdb=" F4 ALF A1502 " pdb="MG MG A1503 " model vdw 1.720 2.120 nonbonded pdb="MG MG A1503 " pdb=" O HOH A1601 " model vdw 1.974 2.170 nonbonded pdb=" OD2 ASP A 560 " pdb="MG MG A1503 " model vdw 1.978 2.170 nonbonded pdb="MG MG A1503 " pdb=" O HOH A1602 " model vdw 2.007 2.170 nonbonded pdb=" OD1 ASP A 954 " pdb="MG MG A1503 " model vdw 2.085 2.170 ... (remaining 91984 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.120 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 33.900 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 11811 Z= 0.219 Angle : 1.132 69.913 16001 Z= 0.453 Chirality : 0.042 0.273 1822 Planarity : 0.005 0.060 1996 Dihedral : 11.940 162.448 4421 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.20 % Allowed : 4.39 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.21), residues: 1410 helix: -1.20 (0.20), residues: 587 sheet: -1.40 (0.34), residues: 202 loop : -2.10 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1132 HIS 0.006 0.001 HIS A 634 PHE 0.010 0.001 PHE C 317 TYR 0.012 0.001 TYR C 141 ARG 0.002 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 196 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 210 average time/residue: 1.2618 time to fit residues: 287.2545 Evaluate side-chains 105 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 1.559 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 1 average time/residue: 0.2997 time to fit residues: 2.2139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN A 409 ASN A 966 HIS A1242 GLN C 305 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11811 Z= 0.214 Angle : 0.786 32.530 16001 Z= 0.341 Chirality : 0.043 0.246 1822 Planarity : 0.005 0.047 1996 Dihedral : 10.440 158.125 1709 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.60 % Rotamer: Outliers : 2.39 % Allowed : 12.29 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.22), residues: 1410 helix: -0.41 (0.21), residues: 592 sheet: -1.04 (0.34), residues: 205 loop : -1.84 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1157 HIS 0.006 0.001 HIS A 634 PHE 0.013 0.001 PHE A 495 TYR 0.020 0.001 TYR C 77 ARG 0.005 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 113 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 131 average time/residue: 1.0896 time to fit residues: 157.0325 Evaluate side-chains 109 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 1.304 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 6 average time/residue: 0.7568 time to fit residues: 6.7824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 114 optimal weight: 0.0270 chunk 127 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 675 ASN A1242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11811 Z= 0.156 Angle : 0.761 33.043 16001 Z= 0.326 Chirality : 0.042 0.221 1822 Planarity : 0.004 0.044 1996 Dihedral : 9.827 150.498 1709 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.60 % Rotamer: Outliers : 3.35 % Allowed : 12.53 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.22), residues: 1410 helix: 0.10 (0.22), residues: 583 sheet: -0.70 (0.35), residues: 199 loop : -1.61 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1172 HIS 0.004 0.001 HIS A 580 PHE 0.009 0.001 PHE A1205 TYR 0.018 0.001 TYR C 77 ARG 0.004 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 101 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 21 residues processed: 128 average time/residue: 0.9308 time to fit residues: 133.1037 Evaluate side-chains 114 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 1.297 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 16 residues processed: 6 average time/residue: 0.3562 time to fit residues: 4.4979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11811 Z= 0.164 Angle : 0.756 31.183 16001 Z= 0.323 Chirality : 0.041 0.204 1822 Planarity : 0.004 0.045 1996 Dihedral : 9.298 151.759 1709 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.02 % Rotamer: Outliers : 3.51 % Allowed : 13.73 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.23), residues: 1410 helix: 0.39 (0.23), residues: 582 sheet: -0.67 (0.35), residues: 206 loop : -1.47 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1172 HIS 0.003 0.001 HIS A 634 PHE 0.028 0.001 PHE A 492 TYR 0.016 0.001 TYR C 77 ARG 0.005 0.000 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 100 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 22 residues processed: 128 average time/residue: 0.8716 time to fit residues: 126.3704 Evaluate side-chains 113 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 1.397 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 17 residues processed: 5 average time/residue: 1.0391 time to fit residues: 7.6888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN C 364 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11811 Z= 0.299 Angle : 0.813 30.977 16001 Z= 0.358 Chirality : 0.045 0.199 1822 Planarity : 0.004 0.042 1996 Dihedral : 9.022 152.302 1709 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.69 % Favored : 96.24 % Rotamer: Outliers : 4.47 % Allowed : 14.21 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.22), residues: 1410 helix: 0.22 (0.22), residues: 582 sheet: -0.72 (0.35), residues: 205 loop : -1.56 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1172 HIS 0.005 0.001 HIS C 150 PHE 0.012 0.002 PHE A 990 TYR 0.016 0.002 TYR C 236 ARG 0.004 0.000 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 99 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 29 residues processed: 134 average time/residue: 0.9224 time to fit residues: 138.9833 Evaluate side-chains 117 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 88 time to evaluate : 1.228 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 19 residues processed: 10 average time/residue: 0.4583 time to fit residues: 7.2415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 9.9990 chunk 122 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11811 Z= 0.204 Angle : 0.789 30.396 16001 Z= 0.340 Chirality : 0.043 0.221 1822 Planarity : 0.004 0.043 1996 Dihedral : 8.755 152.552 1709 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.98 % Favored : 96.95 % Rotamer: Outliers : 3.11 % Allowed : 16.76 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.23), residues: 1410 helix: 0.36 (0.23), residues: 587 sheet: -0.68 (0.35), residues: 206 loop : -1.53 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1172 HIS 0.003 0.001 HIS A 634 PHE 0.016 0.001 PHE A 492 TYR 0.015 0.001 TYR C 77 ARG 0.005 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 95 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 23 residues processed: 124 average time/residue: 1.0675 time to fit residues: 147.3572 Evaluate side-chains 108 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 1.277 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 0.2082 time to fit residues: 2.5723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 76 optimal weight: 0.2980 chunk 135 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11811 Z= 0.224 Angle : 0.798 30.624 16001 Z= 0.343 Chirality : 0.043 0.216 1822 Planarity : 0.004 0.042 1996 Dihedral : 8.696 152.474 1709 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.69 % Favored : 96.24 % Rotamer: Outliers : 2.95 % Allowed : 17.00 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.22), residues: 1410 helix: 0.36 (0.22), residues: 585 sheet: -0.51 (0.36), residues: 199 loop : -1.61 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1172 HIS 0.003 0.001 HIS A 634 PHE 0.011 0.001 PHE C 317 TYR 0.014 0.001 TYR C 141 ARG 0.006 0.000 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 94 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 27 residues processed: 121 average time/residue: 0.9301 time to fit residues: 126.4736 Evaluate side-chains 116 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 89 time to evaluate : 1.263 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 21 residues processed: 6 average time/residue: 0.3351 time to fit residues: 4.2975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 123 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11811 Z= 0.183 Angle : 0.781 30.315 16001 Z= 0.333 Chirality : 0.043 0.234 1822 Planarity : 0.004 0.042 1996 Dihedral : 8.578 152.316 1709 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.12 % Favored : 96.81 % Rotamer: Outliers : 2.71 % Allowed : 17.32 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.23), residues: 1410 helix: 0.50 (0.23), residues: 579 sheet: -0.54 (0.35), residues: 210 loop : -1.44 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A1172 HIS 0.003 0.001 HIS A 634 PHE 0.015 0.001 PHE A 492 TYR 0.014 0.001 TYR C 77 ARG 0.009 0.000 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 93 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 24 residues processed: 119 average time/residue: 0.9809 time to fit residues: 131.4008 Evaluate side-chains 111 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 87 time to evaluate : 1.512 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 22 residues processed: 2 average time/residue: 0.3352 time to fit residues: 3.2023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 99 optimal weight: 0.0170 chunk 38 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11811 Z= 0.152 Angle : 0.779 30.072 16001 Z= 0.332 Chirality : 0.042 0.219 1822 Planarity : 0.004 0.042 1996 Dihedral : 8.400 152.021 1709 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.02 % Rotamer: Outliers : 2.15 % Allowed : 18.04 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.23), residues: 1410 helix: 0.60 (0.23), residues: 585 sheet: -0.44 (0.36), residues: 212 loop : -1.33 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A1172 HIS 0.004 0.001 HIS A 634 PHE 0.011 0.001 PHE C 317 TYR 0.015 0.001 TYR C 77 ARG 0.007 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 23 residues processed: 116 average time/residue: 0.9219 time to fit residues: 120.1621 Evaluate side-chains 109 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 22 residues processed: 2 average time/residue: 0.2362 time to fit residues: 2.5115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 140 optimal weight: 3.9990 chunk 129 optimal weight: 0.4980 chunk 111 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11811 Z= 0.201 Angle : 0.801 30.694 16001 Z= 0.346 Chirality : 0.043 0.244 1822 Planarity : 0.004 0.041 1996 Dihedral : 8.375 151.648 1709 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.55 % Favored : 96.38 % Rotamer: Outliers : 2.15 % Allowed : 18.52 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.23), residues: 1410 helix: 0.59 (0.23), residues: 579 sheet: -0.50 (0.36), residues: 208 loop : -1.35 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A1172 HIS 0.003 0.001 HIS A 634 PHE 0.024 0.001 PHE A 492 TYR 0.013 0.001 TYR C 77 ARG 0.008 0.000 ARG A 866 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 86 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 24 residues processed: 108 average time/residue: 0.9852 time to fit residues: 119.2697 Evaluate side-chains 108 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 1.353 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 22 residues processed: 3 average time/residue: 0.2363 time to fit residues: 2.8190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 14 optimal weight: 0.0980 chunk 20 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 6 optimal weight: 0.0270 chunk 80 optimal weight: 0.6980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.152680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.108243 restraints weight = 16093.138| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.69 r_work: 0.3512 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11811 Z= 0.147 Angle : 0.785 30.048 16001 Z= 0.336 Chirality : 0.042 0.249 1822 Planarity : 0.004 0.041 1996 Dihedral : 8.208 151.267 1709 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.84 % Favored : 97.09 % Rotamer: Outliers : 1.84 % Allowed : 18.99 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.23), residues: 1410 helix: 0.68 (0.23), residues: 585 sheet: -0.33 (0.36), residues: 207 loop : -1.24 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A1172 HIS 0.002 0.001 HIS A 883 PHE 0.011 0.001 PHE C 317 TYR 0.015 0.001 TYR C 77 ARG 0.006 0.000 ARG A 866 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3601.08 seconds wall clock time: 65 minutes 29.85 seconds (3929.85 seconds total)