Starting phenix.real_space_refine on Sun Feb 18 07:58:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgx_14714/02_2024/7zgx_14714.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgx_14714/02_2024/7zgx_14714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgx_14714/02_2024/7zgx_14714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgx_14714/02_2024/7zgx_14714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgx_14714/02_2024/7zgx_14714.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgx_14714/02_2024/7zgx_14714.pdb" } resolution = 2.88 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= 0.002 sd= 0.047 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: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 13245 2.51 5 N 3795 2.21 5 O 4293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 610": "OD1" <-> "OD2" Residue "A TYR 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 822": "OD1" <-> "OD2" Residue "A ASP 842": "OD1" <-> "OD2" Residue "A PHE 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 882": "OE1" <-> "OE2" Residue "A PHE 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 942": "OD1" <-> "OD2" Residue "A PHE 953": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1138": "OD1" <-> "OD2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 677": "OD1" <-> "OD2" Residue "B ASP 731": "OD1" <-> "OD2" Residue "B ASP 735": "OD1" <-> "OD2" Residue "B PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 813": "OD1" <-> "OD2" Residue "B PHE 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 953": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1007": "OD1" <-> "OD2" Residue "B TYR 1101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1119": "OE1" <-> "OE2" Residue "C ASP 274": "OD1" <-> "OD2" Residue "C PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 586": "OE1" <-> "OE2" Residue "C ASP 603": "OD1" <-> "OD2" Residue "C TYR 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 813": "OD1" <-> "OD2" Residue "C TYR 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 953": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1083": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1101": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 21351 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7117 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 30, 'TRANS': 918} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 7117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7117 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 30, 'TRANS': 918} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 7117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7117 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 30, 'TRANS': 918} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 11.05, per 1000 atoms: 0.52 Number of scatterers: 21351 At special positions: 0 Unit cell: (164.418, 155.42, 129.244, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 4293 8.00 N 3795 7.00 C 13245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.30 Conformation dependent library (CDL) restraints added in 4.0 seconds 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4932 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 26 sheets defined 7.0% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 221 through 252 removed outlier: 3.575A pdb=" N THR A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 removed outlier: 3.888A pdb=" N PHE A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.731A pdb=" N THR A 455 " --> pdb=" O THR A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 594 removed outlier: 4.161A pdb=" N ALA A 594 " --> pdb=" O MET A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 875 removed outlier: 4.242A pdb=" N GLY A 875 " --> pdb=" O LEU A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 924 Processing helix chain 'B' and resid 221 through 252 removed outlier: 3.650A pdb=" N THR B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.852A pdb=" N PHE B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 Processing helix chain 'B' and resid 451 through 456 removed outlier: 3.613A pdb=" N THR B 455 " --> pdb=" O THR B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 594 removed outlier: 4.223A pdb=" N ALA B 594 " --> pdb=" O MET B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 787 Processing helix chain 'B' and resid 870 through 875 removed outlier: 4.283A pdb=" N GLY B 875 " --> pdb=" O LEU B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 924 Processing helix chain 'C' and resid 221 through 252 removed outlier: 3.540A pdb=" N GLU C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 308 removed outlier: 3.982A pdb=" N PHE C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 Processing helix chain 'C' and resid 451 through 456 removed outlier: 3.550A pdb=" N THR C 455 " --> pdb=" O THR C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 594 removed outlier: 4.132A pdb=" N ALA C 594 " --> pdb=" O MET C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 787 Processing helix chain 'C' and resid 870 through 875 removed outlier: 3.620A pdb=" N GLY C 873 " --> pdb=" O GLY C 870 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY C 875 " --> pdb=" O LEU C 872 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 255 through 269 removed outlier: 3.743A pdb=" N SER A 383 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N SER A 267 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLU A 381 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR A 269 " --> pdb=" O TYR A 379 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N TYR A 379 " --> pdb=" O THR A 269 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 379 through 393 current: chain 'A' and resid 418 through 420 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 418 through 420 current: chain 'A' and resid 473 through 483 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 473 through 483 current: chain 'A' and resid 756 through 765 removed outlier: 3.799A pdb=" N PHE A 758 " --> pdb=" O THR A 777 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 789 through 792 current: chain 'A' and resid 803 through 814 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 932 through 936 current: chain 'A' and resid 977 through 984 removed outlier: 3.500A pdb=" N ALA A1016 " --> pdb=" O SER A 998 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1057 through 1061 current: chain 'A' and resid 1075 through 1085 removed outlier: 3.831A pdb=" N GLY A1115 " --> pdb=" O ASP A1081 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR A1133 " --> pdb=" O ASN A1114 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1125 through 1134 current: chain 'B' and resid 379 through 393 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 379 through 393 current: chain 'B' and resid 418 through 420 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 418 through 420 current: chain 'B' and resid 473 through 483 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 473 through 483 current: chain 'B' and resid 982 through 984 removed outlier: 3.558A pdb=" N ALA B1016 " --> pdb=" O SER B 998 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1014 through 1022 current: chain 'B' and resid 1054 through 1061 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1054 through 1061 current: chain 'B' and resid 1076 through 1085 removed outlier: 3.584A pdb=" N GLY B1115 " --> pdb=" O ASP B1081 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR B1133 " --> pdb=" O ASN B1114 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1126 through 1134 current: chain 'C' and resid 379 through 394 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 379 through 394 current: chain 'C' and resid 418 through 420 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 418 through 420 current: chain 'C' and resid 982 through 984 removed outlier: 3.725A pdb=" N ALA C1016 " --> pdb=" O SER C 998 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY C1063 " --> pdb=" O ASN C1036 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C1080 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY C1115 " --> pdb=" O ASP C1081 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C1133 " --> pdb=" O ASN C1114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 334 through 337 Processing sheet with id=AA3, first strand: chain 'A' and resid 436 through 438 Processing sheet with id=AA4, first strand: chain 'A' and resid 466 through 467 Processing sheet with id=AA5, first strand: chain 'A' and resid 487 through 490 removed outlier: 5.817A pdb=" N VAL A 562 " --> pdb=" O ARG A 549 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 611 " --> pdb=" O SER A 622 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER A 622 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 650 through 651 removed outlier: 3.858A pdb=" N THR A 650 " --> pdb=" O ASP A 658 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 724 through 729 removed outlier: 6.165A pdb=" N LEU A 724 " --> pdb=" O ILE A 753 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 819 through 821 Processing sheet with id=AA9, first strand: chain 'A' and resid 962 through 963 removed outlier: 3.564A pdb=" N ASP A 972 " --> pdb=" O VAL A 962 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1088 through 1091 Processing sheet with id=AB2, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AB3, first strand: chain 'B' and resid 465 through 467 Processing sheet with id=AB4, first strand: chain 'B' and resid 487 through 490 removed outlier: 5.848A pdb=" N VAL B 562 " --> pdb=" O ARG B 549 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA B 609 " --> pdb=" O TYR B 624 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER B 622 " --> pdb=" O LEU B 611 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.981A pdb=" N THR B 650 " --> pdb=" O ASP B 658 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 672 through 683 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 672 through 683 current: chain 'B' and resid 748 through 765 removed outlier: 3.557A pdb=" N PHE B 758 " --> pdb=" O THR B 777 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR B 774 " --> pdb=" O GLY B 793 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 793 " --> pdb=" O TYR B 774 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 792 " --> pdb=" O THR B 811 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 819 through 821 Processing sheet with id=AB8, first strand: chain 'B' and resid 962 through 963 Processing sheet with id=AB9, first strand: chain 'B' and resid 1088 through 1091 Processing sheet with id=AC1, first strand: chain 'C' and resid 334 through 337 Processing sheet with id=AC2, first strand: chain 'C' and resid 487 through 490 removed outlier: 5.734A pdb=" N VAL C 562 " --> pdb=" O ARG C 549 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 611 " --> pdb=" O SER C 622 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER C 622 " --> pdb=" O LEU C 611 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 650 through 651 removed outlier: 3.837A pdb=" N THR C 650 " --> pdb=" O ASP C 658 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 674 through 681 removed outlier: 6.373A pdb=" N LYS C 761 " --> pdb=" O TYR C 676 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU C 678 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY C 759 " --> pdb=" O LEU C 678 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR C 680 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY C 757 " --> pdb=" O TYR C 680 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 758 " --> pdb=" O THR C 777 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET C 789 " --> pdb=" O SER C 778 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 789 through 792 current: chain 'C' and resid 803 through 814 removed outlier: 6.449A pdb=" N VAL C 962 " --> pdb=" O PHE C 973 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N PHE C 973 " --> pdb=" O VAL C 962 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 724 through 726 removed outlier: 6.069A pdb=" N LEU C 724 " --> pdb=" O ILE C 753 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 819 through 821 Processing sheet with id=AC7, first strand: chain 'C' and resid 880 through 881 removed outlier: 3.687A pdb=" N ARG C 891 " --> pdb=" O SER C 880 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1088 through 1091 596 hydrogen bonds defined for protein. 1575 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: 7.93 Time building geometry restraints manager: 9.02 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: 7370 1.34 - 1.46: 4133 1.46 - 1.57: 10241 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 21774 Sorted by residual: bond pdb=" C PHE B 881 " pdb=" N GLU B 882 " ideal model delta sigma weight residual 1.332 1.362 -0.030 1.46e-02 4.69e+03 4.16e+00 bond pdb=" C TYR C1090 " pdb=" N THR C1091 " ideal model delta sigma weight residual 1.332 1.309 0.023 1.44e-02 4.82e+03 2.65e+00 bond pdb=" C TYR A1090 " pdb=" N THR A1091 " ideal model delta sigma weight residual 1.333 1.310 0.024 1.61e-02 3.86e+03 2.18e+00 bond pdb=" C THR B 439 " pdb=" N ASN B 440 " ideal model delta sigma weight residual 1.334 1.313 0.022 1.52e-02 4.33e+03 2.04e+00 bond pdb=" CA GLY B 387 " pdb=" C GLY B 387 " ideal model delta sigma weight residual 1.520 1.510 0.010 7.30e-03 1.88e+04 2.03e+00 ... (remaining 21769 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.05: 426 107.05 - 113.78: 11520 113.78 - 120.52: 8352 120.52 - 127.26: 9208 127.26 - 134.00: 89 Bond angle restraints: 29595 Sorted by residual: angle pdb=" C ASN C 632 " pdb=" CA ASN C 632 " pdb=" CB ASN C 632 " ideal model delta sigma weight residual 116.54 109.34 7.20 1.15e+00 7.56e-01 3.92e+01 angle pdb=" C THR B 597 " pdb=" CA THR B 597 " pdb=" CB THR B 597 " ideal model delta sigma weight residual 116.54 110.29 6.25 1.15e+00 7.56e-01 2.95e+01 angle pdb=" C THR C 597 " pdb=" CA THR C 597 " pdb=" CB THR C 597 " ideal model delta sigma weight residual 116.54 110.39 6.15 1.15e+00 7.56e-01 2.86e+01 angle pdb=" C THR A 597 " pdb=" CA THR A 597 " pdb=" CB THR A 597 " ideal model delta sigma weight residual 116.54 110.41 6.13 1.15e+00 7.56e-01 2.85e+01 angle pdb=" N VAL C 990 " pdb=" CA VAL C 990 " pdb=" C VAL C 990 " ideal model delta sigma weight residual 113.22 106.77 6.45 1.23e+00 6.61e-01 2.75e+01 ... (remaining 29590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 11623 17.76 - 35.52: 781 35.52 - 53.28: 109 53.28 - 71.05: 20 71.05 - 88.81: 13 Dihedral angle restraints: 12546 sinusoidal: 4599 harmonic: 7947 Sorted by residual: dihedral pdb=" CA TYR C 696 " pdb=" C TYR C 696 " pdb=" N GLY C 697 " pdb=" CA GLY C 697 " ideal model delta harmonic sigma weight residual 180.00 149.82 30.18 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA TYR A 696 " pdb=" C TYR A 696 " pdb=" N GLY A 697 " pdb=" CA GLY A 697 " ideal model delta harmonic sigma weight residual 180.00 151.33 28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA GLN B1086 " pdb=" C GLN B1086 " pdb=" N ASN B1087 " pdb=" CA ASN B1087 " ideal model delta harmonic sigma weight residual -180.00 -152.51 -27.49 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 12543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2094 0.041 - 0.083: 813 0.083 - 0.124: 258 0.124 - 0.165: 33 0.165 - 0.206: 6 Chirality restraints: 3204 Sorted by residual: chirality pdb=" CB ILE B 535 " pdb=" CA ILE B 535 " pdb=" CG1 ILE B 535 " pdb=" CG2 ILE B 535 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB ILE A 262 " pdb=" CA ILE A 262 " pdb=" CG1 ILE A 262 " pdb=" CG2 ILE A 262 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CB ILE C 262 " pdb=" CA ILE C 262 " pdb=" CG1 ILE C 262 " pdb=" CG2 ILE C 262 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.69e-01 ... (remaining 3201 not shown) Planarity restraints: 4017 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 512 " -0.028 2.00e-02 2.50e+03 2.05e-02 7.37e+00 pdb=" CG PHE A 512 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 512 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 512 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 512 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 512 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 512 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 512 " 0.026 2.00e-02 2.50e+03 1.94e-02 6.60e+00 pdb=" CG PHE B 512 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE B 512 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 512 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 512 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 512 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 512 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 468 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO C 469 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 469 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 469 " -0.035 5.00e-02 4.00e+02 ... (remaining 4014 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 982 2.71 - 3.26: 21430 3.26 - 3.80: 33614 3.80 - 4.35: 43816 4.35 - 4.90: 76532 Nonbonded interactions: 176374 Sorted by model distance: nonbonded pdb=" OH TYR B1117 " pdb=" OE1 GLU B1119 " model vdw 2.159 2.440 nonbonded pdb=" OD1 ASP B 307 " pdb=" OH TYR B1090 " model vdw 2.172 2.440 nonbonded pdb=" OD1 ASN A 733 " pdb=" N ASN A 734 " model vdw 2.179 2.520 nonbonded pdb=" OD1 ASP C 307 " pdb=" OH TYR C1090 " model vdw 2.208 2.440 nonbonded pdb=" O ARG B 251 " pdb=" OG SER B 395 " model vdw 2.212 2.440 ... (remaining 176369 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: 7.200 Set stop_for_unknowns flag: 0.010 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: 31.340 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 57.080 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.110 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:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 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 : 0.005 0.045 21774 Z= 0.356 Angle : 0.767 10.330 29595 Z= 0.466 Chirality : 0.048 0.206 3204 Planarity : 0.005 0.062 4017 Dihedral : 12.229 88.806 7614 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.30 % Favored : 88.28 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.11 (0.15), residues: 2841 helix: -1.25 (0.37), residues: 147 sheet: -1.69 (0.15), residues: 1212 loop : -2.48 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 538 HIS 0.004 0.001 HIS B 612 PHE 0.045 0.002 PHE A 512 TYR 0.020 0.002 TYR C 890 ARG 0.006 0.001 ARG C 816 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 2.263 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8328 (t70) cc_final: 0.7994 (t0) REVERT: A 831 ASP cc_start: 0.8144 (p0) cc_final: 0.7907 (p0) REVERT: B 250 GLU cc_start: 0.8218 (pt0) cc_final: 0.7840 (tm-30) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 1.0292 time to fit residues: 90.5550 Evaluate side-chains 44 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 3.9990 chunk 213 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 221 optimal weight: 0.0980 chunk 85 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 256 optimal weight: 8.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 ASN B 570 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.0576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 21774 Z= 0.364 Angle : 0.630 8.050 29595 Z= 0.343 Chirality : 0.047 0.170 3204 Planarity : 0.004 0.058 4017 Dihedral : 5.209 29.211 3189 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.40 % Favored : 88.17 % Rotamer: Outliers : 0.73 % Allowed : 5.65 % Favored : 93.62 % 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: -2.99 (0.15), residues: 2841 helix: -0.84 (0.39), residues: 147 sheet: -1.61 (0.15), residues: 1188 loop : -2.43 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 538 HIS 0.004 0.001 HIS B 621 PHE 0.025 0.002 PHE A 512 TYR 0.017 0.002 TYR A 837 ARG 0.004 0.001 ARG C1022 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 49 time to evaluate : 2.580 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8409 (t70) cc_final: 0.8032 (t0) REVERT: A 665 LYS cc_start: 0.5580 (pptt) cc_final: 0.4879 (pptt) REVERT: B 250 GLU cc_start: 0.8167 (pt0) cc_final: 0.7914 (tm-30) outliers start: 16 outliers final: 10 residues processed: 61 average time/residue: 0.9555 time to fit residues: 72.8008 Evaluate side-chains 52 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain B residue 831 ASP Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 842 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 142 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 213 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 256 optimal weight: 0.5980 chunk 277 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 254 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 205 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 GLN B 570 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21774 Z= 0.161 Angle : 0.541 6.677 29595 Z= 0.293 Chirality : 0.045 0.191 3204 Planarity : 0.004 0.050 4017 Dihedral : 4.816 24.598 3189 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.54 % Favored : 90.07 % Rotamer: Outliers : 1.15 % Allowed : 8.26 % Favored : 90.59 % 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: -2.70 (0.15), residues: 2841 helix: -0.47 (0.40), residues: 147 sheet: -1.36 (0.15), residues: 1155 loop : -2.30 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 538 HIS 0.002 0.001 HIS A 621 PHE 0.019 0.001 PHE A 512 TYR 0.013 0.001 TYR A 837 ARG 0.003 0.000 ARG C1088 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 59 time to evaluate : 2.555 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8376 (t70) cc_final: 0.7959 (t0) REVERT: A 665 LYS cc_start: 0.5520 (pptt) cc_final: 0.4839 (pptt) REVERT: B 565 ARG cc_start: 0.6306 (mtt180) cc_final: 0.5021 (mtm180) REVERT: C 422 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8244 (t70) outliers start: 25 outliers final: 12 residues processed: 79 average time/residue: 0.8213 time to fit residues: 81.7830 Evaluate side-chains 62 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 831 ASP Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 842 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 0.0670 chunk 192 optimal weight: 0.0980 chunk 133 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 257 optimal weight: 2.9990 chunk 272 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 ASN C 400 GLN C 420 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21774 Z= 0.154 Angle : 0.527 7.381 29595 Z= 0.284 Chirality : 0.044 0.161 3204 Planarity : 0.003 0.049 4017 Dihedral : 4.610 22.744 3189 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.96 % Favored : 89.72 % Rotamer: Outliers : 1.42 % Allowed : 9.73 % Favored : 88.84 % 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: -2.54 (0.15), residues: 2841 helix: -0.35 (0.41), residues: 147 sheet: -1.24 (0.15), residues: 1161 loop : -2.20 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 538 HIS 0.001 0.001 HIS B 612 PHE 0.025 0.001 PHE C 512 TYR 0.012 0.001 TYR A 837 ARG 0.004 0.000 ARG C1022 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 55 time to evaluate : 2.436 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8407 (t70) cc_final: 0.8023 (t0) REVERT: A 590 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7358 (ppp) REVERT: A 611 LEU cc_start: 0.8904 (tp) cc_final: 0.8702 (tm) REVERT: B 565 ARG cc_start: 0.6281 (mtt180) cc_final: 0.4916 (mtm180) REVERT: C 422 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8234 (t70) REVERT: C 865 SER cc_start: 0.8331 (m) cc_final: 0.7929 (t) outliers start: 31 outliers final: 20 residues processed: 80 average time/residue: 0.8000 time to fit residues: 81.4499 Evaluate side-chains 72 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 50 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain A residue 1087 ASN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 831 ASP Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1087 ASN Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 842 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 202 optimal weight: 0.1980 chunk 112 optimal weight: 0.9990 chunk 232 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 139 optimal weight: 0.5980 chunk 244 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 GLN ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21774 Z= 0.207 Angle : 0.536 6.668 29595 Z= 0.289 Chirality : 0.044 0.152 3204 Planarity : 0.004 0.049 4017 Dihedral : 4.569 22.889 3189 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.00 % Favored : 89.69 % Rotamer: Outliers : 1.93 % Allowed : 10.65 % Favored : 87.42 % 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: -2.43 (0.15), residues: 2841 helix: -0.28 (0.41), residues: 147 sheet: -1.13 (0.15), residues: 1155 loop : -2.15 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 538 HIS 0.002 0.001 HIS B 621 PHE 0.025 0.001 PHE C 512 TYR 0.013 0.001 TYR A 837 ARG 0.003 0.000 ARG C1022 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 49 time to evaluate : 2.209 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8452 (t70) cc_final: 0.7998 (t0) REVERT: A 590 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7386 (ppp) REVERT: A 1002 THR cc_start: 0.9197 (m) cc_final: 0.8905 (t) REVERT: B 565 ARG cc_start: 0.6353 (mtt180) cc_final: 0.4963 (mtm180) REVERT: C 422 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.8241 (t70) REVERT: C 865 SER cc_start: 0.8356 (OUTLIER) cc_final: 0.7910 (t) outliers start: 42 outliers final: 28 residues processed: 85 average time/residue: 0.7067 time to fit residues: 78.5712 Evaluate side-chains 78 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 47 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain A residue 1087 ASN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 831 ASP Chi-restraints excluded: chain B residue 844 THR Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1087 ASN Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 865 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 91 optimal weight: 0.8980 chunk 245 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 272 optimal weight: 6.9990 chunk 226 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 22 optimal weight: 0.0770 chunk 90 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 overall best weight: 1.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 GLN ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21774 Z= 0.228 Angle : 0.544 12.113 29595 Z= 0.291 Chirality : 0.044 0.151 3204 Planarity : 0.004 0.052 4017 Dihedral : 4.570 22.847 3189 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.49 % Favored : 89.23 % Rotamer: Outliers : 1.97 % Allowed : 11.52 % Favored : 86.50 % 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: -2.38 (0.15), residues: 2841 helix: -0.27 (0.41), residues: 147 sheet: -1.14 (0.15), residues: 1173 loop : -2.09 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 538 HIS 0.002 0.001 HIS B 621 PHE 0.026 0.001 PHE C 512 TYR 0.013 0.001 TYR C1060 ARG 0.003 0.000 ARG C1088 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 48 time to evaluate : 2.425 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8487 (t70) cc_final: 0.8030 (t0) REVERT: A 590 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7395 (ppp) REVERT: A 1002 THR cc_start: 0.9198 (m) cc_final: 0.8902 (t) REVERT: B 565 ARG cc_start: 0.6156 (mtt180) cc_final: 0.5002 (mtm180) REVERT: C 422 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8233 (t70) REVERT: C 865 SER cc_start: 0.8350 (OUTLIER) cc_final: 0.7904 (t) outliers start: 43 outliers final: 30 residues processed: 85 average time/residue: 0.6543 time to fit residues: 73.5216 Evaluate side-chains 81 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 48 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain A residue 1087 ASN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 831 ASP Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 844 THR Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1087 ASN Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 865 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 263 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 229 optimal weight: 0.0060 chunk 152 optimal weight: 3.9990 chunk 271 optimal weight: 0.0970 chunk 170 optimal weight: 0.2980 chunk 165 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 GLN ** B 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21774 Z= 0.155 Angle : 0.516 13.018 29595 Z= 0.276 Chirality : 0.043 0.145 3204 Planarity : 0.003 0.050 4017 Dihedral : 4.415 22.630 3189 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.61 % Favored : 90.14 % Rotamer: Outliers : 1.97 % Allowed : 11.85 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.15), residues: 2841 helix: -0.15 (0.42), residues: 147 sheet: -0.94 (0.16), residues: 1152 loop : -2.06 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 538 HIS 0.002 0.001 HIS C 612 PHE 0.024 0.001 PHE C 512 TYR 0.013 0.001 TYR C1060 ARG 0.003 0.000 ARG C1088 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 53 time to evaluate : 2.398 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8433 (t70) cc_final: 0.7994 (t0) REVERT: A 423 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9014 (tt) REVERT: A 665 LYS cc_start: 0.5079 (OUTLIER) cc_final: 0.4334 (pptt) REVERT: A 1002 THR cc_start: 0.9150 (m) cc_final: 0.8897 (t) REVERT: B 565 ARG cc_start: 0.6238 (mtt180) cc_final: 0.5023 (mtm180) REVERT: C 422 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8221 (t70) REVERT: C 624 TYR cc_start: 0.8211 (t80) cc_final: 0.7813 (t80) outliers start: 43 outliers final: 27 residues processed: 89 average time/residue: 0.6751 time to fit residues: 78.2664 Evaluate side-chains 79 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 49 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain A residue 1087 ASN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 831 ASP Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1087 ASN Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 842 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 168 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 52 optimal weight: 0.0000 chunk 172 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 chunk 213 optimal weight: 1.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 GLN ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21774 Z= 0.171 Angle : 0.523 14.017 29595 Z= 0.278 Chirality : 0.044 0.141 3204 Planarity : 0.003 0.051 4017 Dihedral : 4.380 22.287 3189 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.07 % Favored : 89.79 % Rotamer: Outliers : 2.02 % Allowed : 12.26 % Favored : 85.72 % 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: -2.17 (0.16), residues: 2841 helix: -0.12 (0.42), residues: 147 sheet: -0.97 (0.16), residues: 1179 loop : -1.98 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 538 HIS 0.002 0.001 HIS B 621 PHE 0.024 0.001 PHE C 512 TYR 0.012 0.001 TYR A 837 ARG 0.003 0.000 ARG C1088 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 54 time to evaluate : 2.385 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8457 (t70) cc_final: 0.8014 (t0) REVERT: A 423 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9001 (tt) REVERT: A 590 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7356 (ppp) REVERT: A 665 LYS cc_start: 0.5087 (pptt) cc_final: 0.4350 (pptt) REVERT: A 1002 THR cc_start: 0.9148 (m) cc_final: 0.8872 (t) REVERT: B 565 ARG cc_start: 0.6263 (mtt180) cc_final: 0.5035 (mtm180) REVERT: C 422 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8225 (t70) REVERT: C 624 TYR cc_start: 0.8210 (t80) cc_final: 0.7823 (t80) outliers start: 44 outliers final: 32 residues processed: 92 average time/residue: 0.6810 time to fit residues: 83.2878 Evaluate side-chains 81 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 46 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain A residue 1087 ASN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 831 ASP Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 844 THR Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 1087 ASN Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 1029 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 247 optimal weight: 0.0270 chunk 260 optimal weight: 8.9990 chunk 237 optimal weight: 4.9990 chunk 253 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 228 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 252 optimal weight: 0.9980 overall best weight: 1.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 GLN ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN B 420 GLN ** B 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21774 Z= 0.230 Angle : 0.540 14.129 29595 Z= 0.289 Chirality : 0.044 0.174 3204 Planarity : 0.004 0.052 4017 Dihedral : 4.450 22.455 3189 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.67 % Favored : 89.16 % Rotamer: Outliers : 2.02 % Allowed : 12.44 % Favored : 85.54 % 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: -2.21 (0.16), residues: 2841 helix: -0.66 (0.39), residues: 168 sheet: -0.95 (0.16), residues: 1179 loop : -2.00 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 538 HIS 0.003 0.001 HIS B 621 PHE 0.025 0.001 PHE C 512 TYR 0.013 0.001 TYR A 837 ARG 0.003 0.000 ARG C1088 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 47 time to evaluate : 2.504 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8496 (t70) cc_final: 0.8045 (OUTLIER) REVERT: A 423 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9013 (tt) REVERT: A 590 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7357 (ppp) REVERT: A 1002 THR cc_start: 0.9169 (m) cc_final: 0.8877 (t) REVERT: B 565 ARG cc_start: 0.6196 (mtt180) cc_final: 0.5021 (mtm180) REVERT: C 422 ASP cc_start: 0.8843 (OUTLIER) cc_final: 0.8251 (t70) REVERT: C 624 TYR cc_start: 0.8230 (t80) cc_final: 0.7803 (t80) outliers start: 44 outliers final: 34 residues processed: 86 average time/residue: 0.7631 time to fit residues: 84.2616 Evaluate side-chains 82 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 46 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain A residue 1087 ASN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 831 ASP Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 844 THR Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1087 ASN Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 1029 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 9.9990 chunk 267 optimal weight: 1.9990 chunk 163 optimal weight: 0.0970 chunk 127 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 280 optimal weight: 4.9990 chunk 258 optimal weight: 0.0980 chunk 223 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 GLN ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21774 Z= 0.149 Angle : 0.520 14.560 29595 Z= 0.277 Chirality : 0.044 0.166 3204 Planarity : 0.003 0.050 4017 Dihedral : 4.350 22.298 3189 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.71 % Favored : 90.14 % Rotamer: Outliers : 1.61 % Allowed : 13.09 % Favored : 85.31 % 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: -2.13 (0.16), residues: 2841 helix: -0.50 (0.40), residues: 165 sheet: -0.87 (0.16), residues: 1170 loop : -1.98 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 538 HIS 0.002 0.001 HIS C 612 PHE 0.024 0.001 PHE C 512 TYR 0.012 0.001 TYR A 837 ARG 0.006 0.000 ARG B1022 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 49 time to evaluate : 2.347 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8457 (t70) cc_final: 0.8014 (t0) REVERT: A 423 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8994 (tt) REVERT: A 800 TYR cc_start: 0.7143 (t80) cc_final: 0.6669 (t80) REVERT: A 1002 THR cc_start: 0.9145 (m) cc_final: 0.8883 (t) REVERT: B 565 ARG cc_start: 0.6202 (mtt180) cc_final: 0.5046 (mtm180) REVERT: C 422 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8230 (t70) REVERT: C 624 TYR cc_start: 0.8198 (t80) cc_final: 0.7794 (t80) REVERT: C 789 MET cc_start: 0.8492 (ttt) cc_final: 0.7721 (ttm) outliers start: 35 outliers final: 30 residues processed: 80 average time/residue: 0.7162 time to fit residues: 75.7775 Evaluate side-chains 78 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 46 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain A residue 1087 ASN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 831 ASP Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 844 THR Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 1087 ASN Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 1029 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 0.0770 chunk 238 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 224 optimal weight: 8.9990 chunk 93 optimal weight: 0.2980 chunk 230 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 overall best weight: 1.0744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.073836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.061740 restraints weight = 54124.195| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.86 r_work: 0.3047 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21774 Z= 0.176 Angle : 0.519 14.306 29595 Z= 0.277 Chirality : 0.044 0.155 3204 Planarity : 0.003 0.050 4017 Dihedral : 4.327 21.963 3189 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.93 % Favored : 89.93 % Rotamer: Outliers : 1.79 % Allowed : 13.13 % Favored : 85.08 % 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: -2.06 (0.16), residues: 2841 helix: -0.51 (0.39), residues: 165 sheet: -0.80 (0.16), residues: 1167 loop : -1.95 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 538 HIS 0.002 0.001 HIS B 621 PHE 0.024 0.001 PHE C 512 TYR 0.012 0.001 TYR A 837 ARG 0.006 0.000 ARG B1022 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3995.85 seconds wall clock time: 74 minutes 33.17 seconds (4473.17 seconds total)