Starting phenix.real_space_refine on Sun Feb 18 09:30:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ae1_15378/02_2024/8ae1_15378.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ae1_15378/02_2024/8ae1_15378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ae1_15378/02_2024/8ae1_15378.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ae1_15378/02_2024/8ae1_15378.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ae1_15378/02_2024/8ae1_15378.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ae1_15378/02_2024/8ae1_15378.pdb" } resolution = 3.25 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 18 9.91 5 S 18 5.16 5 C 13332 2.51 5 N 3819 2.21 5 O 4317 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 776": "OD1" <-> "OD2" Residue "A PHE 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 882": "OE1" <-> "OE2" Residue "A PHE 973": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 776": "OD1" <-> "OD2" Residue "B ASP 813": "OD1" <-> "OD2" Residue "B TYR 854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 973": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "C PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 776": "OD1" <-> "OD2" Residue "C TYR 854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 973": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 985": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21504 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7162 Classifications: {'peptide': 953} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 922} Chain: "B" Number of atoms: 7162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7162 Classifications: {'peptide': 953} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 922} Chain: "C" Number of atoms: 7162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7162 Classifications: {'peptide': 953} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 922} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' CA': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' CA': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' CA': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 11.19, per 1000 atoms: 0.52 Number of scatterers: 21504 At special positions: 0 Unit cell: (168.168, 157.248, 136.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 18 19.99 S 18 16.00 O 4317 8.00 N 3819 7.00 C 13332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 896 " - pdb=" SG CYS A 929 " distance=2.03 Simple disulfide: pdb=" SG CYS B 896 " - pdb=" SG CYS B 929 " distance=2.03 Simple disulfide: pdb=" SG CYS C 896 " - pdb=" SG CYS C 929 " distance=2.03 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: 7.90 Conformation dependent library (CDL) restraints added in 4.0 seconds 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4956 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 34 sheets defined 8.9% alpha, 52.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.51 Creating SS restraints... Processing helix chain 'A' and resid 217 through 252 removed outlier: 3.650A pdb=" N ARG A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 removed outlier: 4.231A pdb=" N PHE A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.589A pdb=" N LEU A 325 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.907A pdb=" N TYR A 354 " --> pdb=" O PRO A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.577A pdb=" N THR A 455 " --> pdb=" O THR A 451 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 451 through 456' Processing helix chain 'A' and resid 591 through 596 Processing helix chain 'A' and resid 688 through 693 Processing helix chain 'A' and resid 784 through 788 removed outlier: 3.847A pdb=" N ASN A 787 " --> pdb=" O ASP A 784 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 788 " --> pdb=" O ASN A 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 784 through 788' Processing helix chain 'A' and resid 870 through 875 removed outlier: 3.922A pdb=" N GLY A 875 " --> pdb=" O LEU A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 924 removed outlier: 3.501A pdb=" N GLN A 923 " --> pdb=" O ASN A 920 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 924 " --> pdb=" O LEU A 921 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 920 through 924' Processing helix chain 'B' and resid 217 through 252 removed outlier: 3.693A pdb=" N ARG B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 239 " --> pdb=" O VAL B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 4.199A pdb=" N PHE B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 325 removed outlier: 3.627A pdb=" N LEU B 325 " --> pdb=" O ALA B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.778A pdb=" N TYR B 354 " --> pdb=" O PRO B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 456 removed outlier: 3.557A pdb=" N THR B 455 " --> pdb=" O THR B 451 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B 456 " --> pdb=" O GLY B 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 451 through 456' Processing helix chain 'B' and resid 591 through 596 removed outlier: 3.501A pdb=" N GLN B 595 " --> pdb=" O PHE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 693 Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.908A pdb=" N ASN B 787 " --> pdb=" O ASP B 784 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 788 " --> pdb=" O ASN B 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 784 through 788' Processing helix chain 'B' and resid 870 through 875 removed outlier: 3.887A pdb=" N GLY B 875 " --> pdb=" O LEU B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 924 removed outlier: 3.608A pdb=" N SER B 924 " --> pdb=" O LEU B 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 252 removed outlier: 3.601A pdb=" N ARG C 227 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN C 239 " --> pdb=" O VAL C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 308 removed outlier: 4.219A pdb=" N PHE C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 325 removed outlier: 3.648A pdb=" N LEU C 325 " --> pdb=" O ALA C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 removed outlier: 3.738A pdb=" N TYR C 354 " --> pdb=" O PRO C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 456 removed outlier: 3.586A pdb=" N THR C 455 " --> pdb=" O THR C 451 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR C 456 " --> pdb=" O GLY C 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 451 through 456' Processing helix chain 'C' and resid 591 through 596 Processing helix chain 'C' and resid 688 through 693 Processing helix chain 'C' and resid 784 through 788 removed outlier: 3.870A pdb=" N ASN C 787 " --> pdb=" O ASP C 784 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C 788 " --> pdb=" O ASN C 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 784 through 788' Processing helix chain 'C' and resid 870 through 875 removed outlier: 3.994A pdb=" N GLY C 875 " --> pdb=" O LEU C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 924 removed outlier: 3.618A pdb=" N SER C 924 " --> pdb=" O LEU C 921 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 254 through 256 Processing sheet with id=AA2, first strand: chain 'A' and resid 378 through 384 removed outlier: 4.176A pdb=" N GLY A 382 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER A 265 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR A 384 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY A 263 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE A 262 " --> pdb=" O TYR A1163 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A1163 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR A1060 " --> pdb=" O GLY A1082 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE A1035 " --> pdb=" O THR A1023 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A1016 " --> pdb=" O SER A 998 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 996 " --> pdb=" O GLY A1018 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 980 " --> pdb=" O PHE A 999 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 953 " --> pdb=" O HIS A 939 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 850 " --> pdb=" O GLY A 938 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ALA A 832 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG A 816 " --> pdb=" O ALA A 832 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N VAL A 834 " --> pdb=" O SER A 814 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N SER A 814 " --> pdb=" O VAL A 834 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ARG A 836 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N LEU A 812 " --> pdb=" O ARG A 836 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ALA A 838 " --> pdb=" O ASN A 810 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ASN A 810 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N GLN A 840 " --> pdb=" O THR A 808 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N THR A 808 " --> pdb=" O GLN A 840 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ASP A 842 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ARG A 806 " --> pdb=" O ASP A 842 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 809 " --> pdb=" O GLY A 794 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 792 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR A 790 " --> pdb=" O ASP A 813 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 793 " --> pdb=" O TYR A 774 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 774 " --> pdb=" O GLY A 793 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER A 795 " --> pdb=" O GLY A 772 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY A 772 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL A 769 " --> pdb=" O LEU A 766 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLN A 755 " --> pdb=" O LYS A 682 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS A 682 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY A 757 " --> pdb=" O TYR A 680 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TYR A 680 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY A 759 " --> pdb=" O LEU A 678 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU A 678 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS A 761 " --> pdb=" O TYR A 676 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP A 603 " --> pdb=" O ARG A 630 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL A 562 " --> pdb=" O ARG A 549 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 522 " --> pdb=" O GLY A 500 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 500 " --> pdb=" O GLY A 522 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 389 removed outlier: 4.268A pdb=" N ILE A 262 " --> pdb=" O TYR A1163 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A1163 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR A1060 " --> pdb=" O GLY A1082 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE A1035 " --> pdb=" O THR A1023 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A1016 " --> pdb=" O SER A 998 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 996 " --> pdb=" O GLY A1018 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 980 " --> pdb=" O PHE A 999 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 953 " --> pdb=" O HIS A 939 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 850 " --> pdb=" O GLY A 938 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 342 through 346 removed outlier: 3.950A pdb=" N SER A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AA6, first strand: chain 'A' and resid 426 through 428 Processing sheet with id=AA7, first strand: chain 'A' and resid 436 through 438 Processing sheet with id=AA8, first strand: chain 'A' and resid 465 through 467 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 476 Processing sheet with id=AB1, first strand: chain 'A' and resid 505 through 506 Processing sheet with id=AB2, first strand: chain 'A' and resid 725 through 729 Processing sheet with id=AB3, first strand: chain 'A' and resid 879 through 880 removed outlier: 3.535A pdb=" N ARG A 891 " --> pdb=" O SER A 880 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 962 through 963 removed outlier: 3.541A pdb=" N ASP A 972 " --> pdb=" O VAL A 962 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1088 through 1091 Processing sheet with id=AB6, first strand: chain 'A' and resid 1165 through 1166 Processing sheet with id=AB7, first strand: chain 'B' and resid 378 through 384 removed outlier: 4.102A pdb=" N GLY B 382 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER B 265 " --> pdb=" O GLY B 382 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR B 384 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY B 263 " --> pdb=" O THR B 384 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE B 262 " --> pdb=" O TYR B1163 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR B1163 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR B1060 " --> pdb=" O GLY B1082 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B1053 " --> pdb=" O ASN B1046 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE B1035 " --> pdb=" O THR B1023 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B1016 " --> pdb=" O SER B 998 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 996 " --> pdb=" O GLY B1018 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 980 " --> pdb=" O PHE B 999 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 953 " --> pdb=" O HIS B 939 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 932 " --> pdb=" O ARG B 856 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE B 850 " --> pdb=" O GLY B 938 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ALA B 832 " --> pdb=" O ARG B 816 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ARG B 816 " --> pdb=" O ALA B 832 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL B 834 " --> pdb=" O SER B 814 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N SER B 814 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ARG B 836 " --> pdb=" O LEU B 812 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N LEU B 812 " --> pdb=" O ARG B 836 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ALA B 838 " --> pdb=" O ASN B 810 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N ASN B 810 " --> pdb=" O ALA B 838 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N GLN B 840 " --> pdb=" O THR B 808 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N THR B 808 " --> pdb=" O GLN B 840 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ASP B 842 " --> pdb=" O ARG B 806 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ARG B 806 " --> pdb=" O ASP B 842 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 809 " --> pdb=" O GLY B 794 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 792 " --> pdb=" O THR B 811 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR B 790 " --> pdb=" O ASP B 813 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 795 " --> pdb=" O GLY B 772 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY B 772 " --> pdb=" O SER B 795 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL B 769 " --> pdb=" O LEU B 766 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ALA B 763 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU B 675 " --> pdb=" O ALA B 763 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASN B 765 " --> pdb=" O VAL B 673 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N VAL B 673 " --> pdb=" O ASN B 765 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP B 603 " --> pdb=" O ARG B 630 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL B 562 " --> pdb=" O ARG B 549 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY B 522 " --> pdb=" O GLY B 500 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 500 " --> pdb=" O GLY B 522 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 387 through 389 removed outlier: 4.223A pdb=" N ILE B 262 " --> pdb=" O TYR B1163 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR B1163 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR B1060 " --> pdb=" O GLY B1082 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B1053 " --> pdb=" O ASN B1046 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE B1035 " --> pdb=" O THR B1023 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B1016 " --> pdb=" O SER B 998 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 996 " --> pdb=" O GLY B1018 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 980 " --> pdb=" O PHE B 999 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 953 " --> pdb=" O HIS B 939 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 932 " --> pdb=" O ARG B 856 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE B 850 " --> pdb=" O GLY B 938 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 342 through 346 removed outlier: 3.902A pdb=" N SER B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 465 through 467 Processing sheet with id=AC2, first strand: chain 'B' and resid 473 through 476 removed outlier: 7.416A pdb=" N PHE C 425 " --> pdb=" O THR C 394 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR C 394 " --> pdb=" O PHE C 425 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 505 through 506 Processing sheet with id=AC4, first strand: chain 'B' and resid 725 through 729 Processing sheet with id=AC5, first strand: chain 'B' and resid 879 through 880 Processing sheet with id=AC6, first strand: chain 'B' and resid 962 through 963 removed outlier: 3.567A pdb=" N ASP B 972 " --> pdb=" O VAL B 962 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1088 through 1091 Processing sheet with id=AC8, first strand: chain 'B' and resid 1165 through 1166 Processing sheet with id=AC9, first strand: chain 'C' and resid 378 through 384 removed outlier: 4.220A pdb=" N GLY C 382 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER C 265 " --> pdb=" O GLY C 382 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR C 384 " --> pdb=" O GLY C 263 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY C 263 " --> pdb=" O THR C 384 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE C 262 " --> pdb=" O TYR C1163 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR C1163 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE C1035 " --> pdb=" O THR C1023 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C1016 " --> pdb=" O SER C 998 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 996 " --> pdb=" O GLY C1018 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 980 " --> pdb=" O PHE C 999 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE C 953 " --> pdb=" O HIS C 939 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER C 932 " --> pdb=" O ARG C 856 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE C 850 " --> pdb=" O GLY C 938 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ALA C 832 " --> pdb=" O ARG C 816 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG C 816 " --> pdb=" O ALA C 832 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N VAL C 834 " --> pdb=" O SER C 814 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N SER C 814 " --> pdb=" O VAL C 834 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ARG C 836 " --> pdb=" O LEU C 812 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N LEU C 812 " --> pdb=" O ARG C 836 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ALA C 838 " --> pdb=" O ASN C 810 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ASN C 810 " --> pdb=" O ALA C 838 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N GLN C 840 " --> pdb=" O THR C 808 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N THR C 808 " --> pdb=" O GLN C 840 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N ASP C 842 " --> pdb=" O ARG C 806 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ARG C 806 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR C 809 " --> pdb=" O GLY C 794 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR C 790 " --> pdb=" O ASP C 813 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER C 795 " --> pdb=" O GLY C 772 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY C 772 " --> pdb=" O SER C 795 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL C 769 " --> pdb=" O LEU C 766 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA C 763 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU C 675 " --> pdb=" O ALA C 763 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ASN C 765 " --> pdb=" O VAL C 673 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL C 673 " --> pdb=" O ASN C 765 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP C 603 " --> pdb=" O ARG C 630 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N VAL C 562 " --> pdb=" O ARG C 549 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY C 522 " --> pdb=" O GLY C 500 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C 500 " --> pdb=" O GLY C 522 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 387 through 389 removed outlier: 4.258A pdb=" N ILE C 262 " --> pdb=" O TYR C1163 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR C1163 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE C1035 " --> pdb=" O THR C1023 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C1016 " --> pdb=" O SER C 998 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 996 " --> pdb=" O GLY C1018 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 980 " --> pdb=" O PHE C 999 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE C 953 " --> pdb=" O HIS C 939 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER C 932 " --> pdb=" O ARG C 856 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE C 850 " --> pdb=" O GLY C 938 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 342 through 346 removed outlier: 3.948A pdb=" N SER C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AD4, first strand: chain 'C' and resid 725 through 729 Processing sheet with id=AD5, first strand: chain 'C' and resid 879 through 880 Processing sheet with id=AD6, first strand: chain 'C' and resid 962 through 963 removed outlier: 3.526A pdb=" N ASP C 972 " --> pdb=" O VAL C 962 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1088 through 1091 1312 hydrogen bonds defined for protein. 3597 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: 11.88 Time building geometry restraints manager: 8.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7431 1.34 - 1.46: 4899 1.46 - 1.58: 9552 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 21912 Sorted by residual: bond pdb=" CG PRO B 494 " pdb=" CD PRO B 494 " ideal model delta sigma weight residual 1.512 1.483 0.029 2.70e-02 1.37e+03 1.12e+00 bond pdb=" CG PRO A 494 " pdb=" CD PRO A 494 " ideal model delta sigma weight residual 1.512 1.484 0.028 2.70e-02 1.37e+03 1.09e+00 bond pdb=" CA THR B1001 " pdb=" CB THR B1001 " ideal model delta sigma weight residual 1.525 1.543 -0.018 1.77e-02 3.19e+03 1.07e+00 bond pdb=" CG PRO C 494 " pdb=" CD PRO C 494 " ideal model delta sigma weight residual 1.512 1.484 0.028 2.70e-02 1.37e+03 1.05e+00 bond pdb=" CA VAL A1029 " pdb=" CB VAL A1029 " ideal model delta sigma weight residual 1.546 1.537 0.009 8.80e-03 1.29e+04 9.98e-01 ... (remaining 21907 not shown) Histogram of bond angle deviations from ideal: 100.65 - 107.31: 441 107.31 - 113.97: 11628 113.97 - 120.64: 8508 120.64 - 127.30: 9110 127.30 - 133.96: 94 Bond angle restraints: 29781 Sorted by residual: angle pdb=" C ALA C 634 " pdb=" N ASN C 635 " pdb=" CA ASN C 635 " ideal model delta sigma weight residual 121.54 127.27 -5.73 1.91e+00 2.74e-01 9.01e+00 angle pdb=" C LEU A1139 " pdb=" N ASN A1140 " pdb=" CA ASN A1140 " ideal model delta sigma weight residual 123.91 128.13 -4.22 1.66e+00 3.63e-01 6.47e+00 angle pdb=" N ASP B 513 " pdb=" CA ASP B 513 " pdb=" C ASP B 513 " ideal model delta sigma weight residual 109.71 106.22 3.49 1.41e+00 5.03e-01 6.12e+00 angle pdb=" C LEU B1139 " pdb=" N ASN B1140 " pdb=" CA ASN B1140 " ideal model delta sigma weight residual 123.91 127.93 -4.02 1.66e+00 3.63e-01 5.88e+00 angle pdb=" C ALA A 634 " pdb=" N ASN A 635 " pdb=" CA ASN A 635 " ideal model delta sigma weight residual 121.54 126.09 -4.55 1.91e+00 2.74e-01 5.67e+00 ... (remaining 29776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 11550 17.00 - 34.01: 869 34.01 - 51.01: 176 51.01 - 68.01: 25 68.01 - 85.01: 19 Dihedral angle restraints: 12639 sinusoidal: 4656 harmonic: 7983 Sorted by residual: dihedral pdb=" CA VAL C 511 " pdb=" C VAL C 511 " pdb=" N PHE C 512 " pdb=" CA PHE C 512 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA VAL A 511 " pdb=" C VAL A 511 " pdb=" N PHE A 512 " pdb=" CA PHE A 512 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA PRO A 469 " pdb=" C PRO A 469 " pdb=" N ALA A 470 " pdb=" CA ALA A 470 " ideal model delta harmonic sigma weight residual -180.00 -160.49 -19.51 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 12636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2365 0.041 - 0.082: 558 0.082 - 0.123: 278 0.123 - 0.164: 17 0.164 - 0.205: 4 Chirality restraints: 3222 Sorted by residual: chirality pdb=" CB ILE B 693 " pdb=" CA ILE B 693 " pdb=" CG1 ILE B 693 " pdb=" CG2 ILE B 693 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ASN C1140 " pdb=" N ASN C1140 " pdb=" C ASN C1140 " pdb=" CB ASN C1140 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA ASN B1140 " pdb=" N ASN B1140 " pdb=" C ASN B1140 " pdb=" CB ASN B1140 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 3219 not shown) Planarity restraints: 4044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 512 " 0.013 2.00e-02 2.50e+03 1.06e-02 1.97e+00 pdb=" CG PHE A 512 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 512 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 512 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 512 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 512 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 512 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 512 " -0.012 2.00e-02 2.50e+03 9.90e-03 1.71e+00 pdb=" CG PHE C 512 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE C 512 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 512 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 512 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 512 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 512 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 468 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO A 469 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 469 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 469 " -0.017 5.00e-02 4.00e+02 ... (remaining 4041 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 823 2.71 - 3.26: 20197 3.26 - 3.81: 32447 3.81 - 4.35: 42220 4.35 - 4.90: 75873 Nonbonded interactions: 171560 Sorted by model distance: nonbonded pdb=" O CYS B 896 " pdb=" ND2 ASN B 900 " model vdw 2.165 2.520 nonbonded pdb=" O CYS C 896 " pdb=" ND2 ASN C 900 " model vdw 2.174 2.520 nonbonded pdb=" OG SER B 267 " pdb=" O PHE B 311 " model vdw 2.174 2.440 nonbonded pdb=" O CYS A 896 " pdb=" ND2 ASN A 900 " model vdw 2.174 2.520 nonbonded pdb=" OG SER C 267 " pdb=" O PHE C 311 " model vdw 2.174 2.440 ... (remaining 171555 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.850 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: 8.470 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 63.290 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.280 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 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 : 0.002 0.029 21912 Z= 0.154 Angle : 0.469 6.836 29781 Z= 0.261 Chirality : 0.044 0.205 3222 Planarity : 0.003 0.041 4044 Dihedral : 12.787 85.014 7674 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.01 (0.16), residues: 2853 helix: -0.65 (0.39), residues: 183 sheet: -0.39 (0.15), residues: 1236 loop : -0.83 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 538 HIS 0.003 0.001 HIS B 939 PHE 0.024 0.001 PHE A 512 TYR 0.010 0.001 TYR A 890 ARG 0.009 0.000 ARG A 891 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 2.206 Fit side-chains REVERT: A 789 MET cc_start: 0.9144 (ttp) cc_final: 0.8938 (ttt) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.3698 time to fit residues: 42.8608 Evaluate side-chains 44 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 2.9990 chunk 216 optimal weight: 0.6980 chunk 119 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 145 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 258 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21912 Z= 0.321 Angle : 0.565 5.809 29781 Z= 0.318 Chirality : 0.047 0.168 3222 Planarity : 0.004 0.048 4044 Dihedral : 4.350 19.857 3207 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.32 % Allowed : 4.55 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.65 (0.16), residues: 2853 helix: 0.32 (0.42), residues: 168 sheet: -0.12 (0.15), residues: 1197 loop : -0.72 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 538 HIS 0.006 0.002 HIS B 939 PHE 0.024 0.002 PHE A 512 TYR 0.017 0.001 TYR C1053 ARG 0.004 0.000 ARG A 891 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 2.544 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 56 average time/residue: 0.3677 time to fit residues: 33.5517 Evaluate side-chains 47 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain C residue 1096 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 259 optimal weight: 0.7980 chunk 280 optimal weight: 3.9990 chunk 230 optimal weight: 0.9990 chunk 257 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 208 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN ** C 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21912 Z= 0.246 Angle : 0.521 5.604 29781 Z= 0.291 Chirality : 0.045 0.164 3222 Planarity : 0.003 0.046 4044 Dihedral : 4.282 18.157 3207 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.32 % Allowed : 7.92 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.54 (0.16), residues: 2853 helix: 0.60 (0.42), residues: 168 sheet: -0.02 (0.15), residues: 1197 loop : -0.69 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 538 HIS 0.005 0.001 HIS A 939 PHE 0.022 0.001 PHE A 512 TYR 0.014 0.001 TYR A 837 ARG 0.005 0.000 ARG A 415 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 2.218 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 53 average time/residue: 0.3861 time to fit residues: 32.6921 Evaluate side-chains 45 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 990 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 3.9990 chunk 194 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 400 GLN B1136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21912 Z= 0.252 Angle : 0.513 5.299 29781 Z= 0.286 Chirality : 0.045 0.159 3222 Planarity : 0.003 0.048 4044 Dihedral : 4.265 17.390 3207 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.55 % Allowed : 9.47 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.51 (0.16), residues: 2853 helix: 0.70 (0.42), residues: 168 sheet: 0.00 (0.15), residues: 1197 loop : -0.69 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 538 HIS 0.005 0.002 HIS B 939 PHE 0.019 0.001 PHE A 512 TYR 0.013 0.001 TYR A 837 ARG 0.003 0.000 ARG A 415 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 2.544 Fit side-chains REVERT: A 585 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8040 (tt0) outliers start: 12 outliers final: 5 residues processed: 61 average time/residue: 0.3776 time to fit residues: 37.6247 Evaluate side-chains 49 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 990 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 205 optimal weight: 0.0870 chunk 113 optimal weight: 6.9990 chunk 235 optimal weight: 0.4980 chunk 190 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 0.8980 chunk 247 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 400 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21912 Z= 0.219 Angle : 0.496 5.083 29781 Z= 0.277 Chirality : 0.045 0.157 3222 Planarity : 0.003 0.047 4044 Dihedral : 4.180 16.375 3207 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.28 % Allowed : 9.70 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.44 (0.16), residues: 2853 helix: 0.83 (0.43), residues: 168 sheet: 0.06 (0.15), residues: 1197 loop : -0.67 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 538 HIS 0.004 0.001 HIS A 939 PHE 0.018 0.001 PHE A 512 TYR 0.013 0.001 TYR A 933 ARG 0.006 0.000 ARG A 415 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 47 time to evaluate : 2.337 Fit side-chains REVERT: A 585 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8081 (tt0) outliers start: 28 outliers final: 13 residues processed: 75 average time/residue: 0.3579 time to fit residues: 43.4020 Evaluate side-chains 57 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 43 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 967 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 275 optimal weight: 5.9990 chunk 228 optimal weight: 0.0980 chunk 127 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 400 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21912 Z= 0.211 Angle : 0.492 4.878 29781 Z= 0.274 Chirality : 0.045 0.202 3222 Planarity : 0.003 0.048 4044 Dihedral : 4.134 16.525 3207 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.37 % Allowed : 10.70 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.40 (0.16), residues: 2853 helix: 0.94 (0.43), residues: 168 sheet: 0.12 (0.15), residues: 1185 loop : -0.68 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 538 HIS 0.004 0.001 HIS B 939 PHE 0.017 0.001 PHE A 512 TYR 0.012 0.001 TYR A 933 ARG 0.006 0.000 ARG A 415 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 44 time to evaluate : 2.555 Fit side-chains REVERT: A 585 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: A 785 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8331 (t0) outliers start: 30 outliers final: 21 residues processed: 74 average time/residue: 0.3629 time to fit residues: 43.4690 Evaluate side-chains 66 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 43 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1069 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 201 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 274 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 chunk 167 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 400 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21912 Z= 0.317 Angle : 0.533 4.879 29781 Z= 0.297 Chirality : 0.046 0.198 3222 Planarity : 0.004 0.049 4044 Dihedral : 4.372 18.094 3207 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.55 % Allowed : 11.70 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.52 (0.16), residues: 2853 helix: 0.81 (0.42), residues: 168 sheet: 0.01 (0.15), residues: 1197 loop : -0.72 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 538 HIS 0.006 0.002 HIS B 939 PHE 0.022 0.002 PHE A 512 TYR 0.016 0.001 TYR A 837 ARG 0.007 0.000 ARG A 415 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 43 time to evaluate : 2.566 Fit side-chains REVERT: A 585 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: A 785 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8238 (t0) outliers start: 34 outliers final: 26 residues processed: 76 average time/residue: 0.3534 time to fit residues: 43.5280 Evaluate side-chains 68 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 40 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1069 PHE Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1069 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 0.3980 chunk 109 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 174 optimal weight: 0.7980 chunk 187 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 400 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21912 Z= 0.138 Angle : 0.470 4.750 29781 Z= 0.262 Chirality : 0.044 0.181 3222 Planarity : 0.003 0.045 4044 Dihedral : 3.991 16.395 3207 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.00 % Allowed : 12.39 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.31 (0.16), residues: 2853 helix: 1.14 (0.43), residues: 168 sheet: 0.18 (0.15), residues: 1185 loop : -0.64 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 538 HIS 0.002 0.001 HIS C 612 PHE 0.014 0.001 PHE A 512 TYR 0.012 0.001 TYR A1060 ARG 0.007 0.000 ARG A 415 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 47 time to evaluate : 2.480 Fit side-chains REVERT: A 585 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: A 671 PHE cc_start: 0.6683 (m-10) cc_final: 0.6472 (t80) REVERT: A 766 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.7888 (tp) REVERT: A 785 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8215 (t0) outliers start: 22 outliers final: 13 residues processed: 69 average time/residue: 0.3683 time to fit residues: 40.9705 Evaluate side-chains 59 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1069 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 0.9980 chunk 240 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 242 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 270 optimal weight: 0.9980 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 400 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 21912 Z= 0.432 Angle : 0.580 5.326 29781 Z= 0.323 Chirality : 0.048 0.201 3222 Planarity : 0.004 0.056 4044 Dihedral : 4.550 18.939 3207 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.46 % Allowed : 12.20 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.58 (0.16), residues: 2853 helix: 0.67 (0.42), residues: 168 sheet: -0.03 (0.15), residues: 1197 loop : -0.76 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 538 HIS 0.008 0.002 HIS B 939 PHE 0.026 0.002 PHE A 512 TYR 0.020 0.002 TYR A 837 ARG 0.008 0.001 ARG A 415 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 46 time to evaluate : 2.410 Fit side-chains REVERT: A 585 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: A 671 PHE cc_start: 0.6712 (m-10) cc_final: 0.6433 (t80) REVERT: A 785 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8243 (t0) outliers start: 32 outliers final: 25 residues processed: 78 average time/residue: 0.3654 time to fit residues: 45.0794 Evaluate side-chains 70 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 43 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1069 PHE Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1069 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 188 optimal weight: 0.9980 chunk 283 optimal weight: 0.9990 chunk 261 optimal weight: 0.5980 chunk 226 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 174 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 240 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 400 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 21912 Z= 0.144 Angle : 0.479 4.705 29781 Z= 0.267 Chirality : 0.044 0.188 3222 Planarity : 0.003 0.045 4044 Dihedral : 4.062 16.380 3207 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.82 % Allowed : 12.89 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.32 (0.16), residues: 2853 helix: 1.13 (0.43), residues: 168 sheet: 0.18 (0.15), residues: 1185 loop : -0.64 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 538 HIS 0.002 0.001 HIS B 939 PHE 0.015 0.001 PHE A 512 TYR 0.011 0.001 TYR A 933 ARG 0.009 0.000 ARG A 415 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 43 time to evaluate : 2.554 Fit side-chains REVERT: A 585 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: A 766 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.7882 (tp) outliers start: 18 outliers final: 15 residues processed: 61 average time/residue: 0.4055 time to fit residues: 39.7587 Evaluate side-chains 60 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 43 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1069 PHE Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1069 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 0.9980 chunk 208 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 226 optimal weight: 8.9990 chunk 94 optimal weight: 0.5980 chunk 232 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 41 optimal weight: 0.3980 chunk 198 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 400 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.093458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.074384 restraints weight = 33383.078| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.04 r_work: 0.2845 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21912 Z= 0.189 Angle : 0.485 4.700 29781 Z= 0.270 Chirality : 0.044 0.197 3222 Planarity : 0.003 0.047 4044 Dihedral : 4.056 16.473 3207 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.09 % Allowed : 12.66 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.31 (0.16), residues: 2853 helix: 1.11 (0.43), residues: 168 sheet: 0.19 (0.15), residues: 1185 loop : -0.64 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 538 HIS 0.003 0.001 HIS B 939 PHE 0.018 0.001 PHE A 512 TYR 0.013 0.001 TYR A1060 ARG 0.009 0.000 ARG A 415 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3340.33 seconds wall clock time: 62 minutes 19.16 seconds (3739.16 seconds total)