Starting phenix.real_space_refine on Thu Jun 27 02:27:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enp_19837/06_2024/9enp_19837_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enp_19837/06_2024/9enp_19837.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enp_19837/06_2024/9enp_19837_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enp_19837/06_2024/9enp_19837_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enp_19837/06_2024/9enp_19837_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enp_19837/06_2024/9enp_19837.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enp_19837/06_2024/9enp_19837.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enp_19837/06_2024/9enp_19837_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enp_19837/06_2024/9enp_19837_neut_updated.pdb" } resolution = 2.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 50 5.49 5 S 49 5.16 5 C 7212 2.51 5 N 2035 2.21 5 O 2204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ARG 112": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 125": "NH1" <-> "NH2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A ARG 430": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 571": "NH1" <-> "NH2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "A ARG 611": "NH1" <-> "NH2" Residue "A ARG 620": "NH1" <-> "NH2" Residue "A ARG 627": "NH1" <-> "NH2" Residue "A ARG 700": "NH1" <-> "NH2" Residue "A ARG 739": "NH1" <-> "NH2" Residue "A ARG 760": "NH1" <-> "NH2" Residue "A ARG 761": "NH1" <-> "NH2" Residue "A ARG 770": "NH1" <-> "NH2" Residue "A ARG 779": "NH1" <-> "NH2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 791": "NH1" <-> "NH2" Residue "A ARG 842": "NH1" <-> "NH2" Residue "A ARG 849": "NH1" <-> "NH2" Residue "A ARG 855": "NH1" <-> "NH2" Residue "A ARG 873": "NH1" <-> "NH2" Residue "A ARG 881": "NH1" <-> "NH2" Residue "A ARG 895": "NH1" <-> "NH2" Residue "A ARG 915": "NH1" <-> "NH2" Residue "A ARG 959": "NH1" <-> "NH2" Residue "A ARG 968": "NH1" <-> "NH2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A ARG 993": "NH1" <-> "NH2" Residue "A ARG 1001": "NH1" <-> "NH2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1020": "NH1" <-> "NH2" Residue "A ARG 1026": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1042": "NH1" <-> "NH2" Residue "A ARG 1048": "NH1" <-> "NH2" Residue "A ARG 1061": "NH1" <-> "NH2" Residue "A ARG 1062": "NH1" <-> "NH2" Residue "A ARG 1071": "NH1" <-> "NH2" Residue "A ARG 1081": "NH1" <-> "NH2" Residue "A ARG 1089": "NH1" <-> "NH2" Residue "A ARG 1094": "NH1" <-> "NH2" Residue "A ARG 1135": "NH1" <-> "NH2" Residue "A ARG 1190": "NH1" <-> "NH2" Residue "A ARG 1205": "NH1" <-> "NH2" Residue "A ARG 1207": "NH1" <-> "NH2" Residue "A ARG 1224": "NH1" <-> "NH2" Residue "A ARG 1225": "NH1" <-> "NH2" Residue "A ARG 1229": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 64": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 106": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ARG 179": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ARG 279": "NH1" <-> "NH2" Residue "B ARG 280": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 11552 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1072, 8446 Classifications: {'peptide': 1072} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 52, 'TRANS': 1017} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 1072, 8446 Classifications: {'peptide': 1072} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 52, 'TRANS': 1017} Chain breaks: 3 bond proxies already assigned to first conformer: 8619 Chain: "B" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2049 Classifications: {'peptide': 266} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 251} Chain breaks: 1 Chain: "C" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 523 Unusual residues: {' AS': 2} Classifications: {'DNA': 24, 'undetermined': 2} Link IDs: {'rna3p': 23, None: 2} Not linked: pdbres=" DC C 21 " pdbres=" AS C 22 " Not linked: pdbres=" AS C 22 " pdbres=" AS C 23 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "D" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 503 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 8 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 7, 7 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2, 'water': 5} Link IDs: {None: 6} Conformer: "B" Number of residues, atoms: 7, 7 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2, 'water': 5} Link IDs: {None: 6} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ATYR A 577 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 577 " occ=0.50 residue: pdb=" N AGLN A 580 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 580 " occ=0.50 residue: pdb=" O AHOH A1401 " occ=0.50 pdb=" O BHOH A1401 " occ=0.50 Time building chain proxies: 12.04, per 1000 atoms: 1.04 Number of scatterers: 11552 At special positions: 0 Unit cell: (83.2, 113.6, 160.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 49 16.00 P 50 15.00 O 2204 8.00 N 2035 7.00 C 7212 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.68 Conformation dependent library (CDL) restraints added in 3.4 seconds 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2496 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 14 sheets defined 35.1% alpha, 19.7% beta 23 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 5.45 Creating SS restraints... Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 169 through 175 removed outlier: 3.740A pdb=" N ALA A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 276 through 285 removed outlier: 4.407A pdb=" N ASP A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 305 Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 421 through 429 Processing helix chain 'A' and resid 443 through 457 Processing helix chain 'A' and resid 471 through 481 Processing helix chain 'A' and resid 525 through 532 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 557 through 566 Proline residue: A 561 - end of helix Processing helix chain 'A' and resid 568 through 592 Processing helix chain 'A' and resid 594 through 605 Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'A' and resid 618 through 631 Processing helix chain 'A' and resid 721 through 729 Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 773 through 794 removed outlier: 3.523A pdb=" N ARG A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) Proline residue: A 793 - end of helix Processing helix chain 'A' and resid 797 through 822 removed outlier: 3.703A pdb=" N VAL A 801 " --> pdb=" O PRO A 797 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 817 " --> pdb=" O VAL A 813 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TYR A 818 " --> pdb=" O CYS A 814 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLY A 819 " --> pdb=" O ASN A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 855 Processing helix chain 'A' and resid 859 through 865 Processing helix chain 'A' and resid 867 through 872 removed outlier: 3.615A pdb=" N ALA A 870 " --> pdb=" O PRO A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 917 removed outlier: 3.561A pdb=" N LYS A 908 " --> pdb=" O ALA A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 979 Processing helix chain 'A' and resid 981 through 992 removed outlier: 3.640A pdb=" N LEU A 990 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA A 991 " --> pdb=" O ALA A 987 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU A 992 " --> pdb=" O ALA A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1000 Processing helix chain 'A' and resid 1008 through 1022 removed outlier: 3.801A pdb=" N VAL A1013 " --> pdb=" O ALA A1009 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A1014 " --> pdb=" O PHE A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1031 Processing helix chain 'A' and resid 1041 through 1043 No H-bonds generated for 'chain 'A' and resid 1041 through 1043' Processing helix chain 'A' and resid 1051 through 1059 Processing helix chain 'A' and resid 1083 through 1086 No H-bonds generated for 'chain 'A' and resid 1083 through 1086' Processing helix chain 'A' and resid 1090 through 1092 No H-bonds generated for 'chain 'A' and resid 1090 through 1092' Processing helix chain 'A' and resid 1146 through 1151 Processing helix chain 'A' and resid 1158 through 1177 removed outlier: 3.832A pdb=" N VAL A1171 " --> pdb=" O GLY A1167 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR A1172 " --> pdb=" O ALA A1168 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA A1175 " --> pdb=" O VAL A1171 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU A1176 " --> pdb=" O THR A1172 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A1177 " --> pdb=" O PHE A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1191 removed outlier: 4.105A pdb=" N PHE A1191 " --> pdb=" O LEU A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1208 Processing helix chain 'A' and resid 1220 through 1233 Processing helix chain 'B' and resid 37 through 48 Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 108 through 112 removed outlier: 4.148A pdb=" N VAL B 111 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 182 through 191 removed outlier: 3.587A pdb=" N THR B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LYS B 187 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 280 removed outlier: 3.642A pdb=" N ARG B 279 " --> pdb=" O ARG B 275 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 74 through 79 Processing sheet with id= B, first strand: chain 'A' and resid 104 through 107 Processing sheet with id= C, first strand: chain 'A' and resid 350 through 352 removed outlier: 7.045A pdb=" N LEU A 185 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE A 152 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR A 183 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU A 154 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL A 181 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL A 156 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY A 179 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A 341 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N HIS A 197 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE A 343 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N TYR A 199 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N CYS A 345 " --> pdb=" O TYR A 199 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 203 through 208 removed outlier: 3.646A pdb=" N GLN A 203 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 521 through 524 removed outlier: 4.036A pdb=" N GLY A 464 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LYS A 372 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL A 391 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 392 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP A 400 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU A 406 " --> pdb=" O ASP A 400 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A 436 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N SER A 413 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU A 438 " --> pdb=" O SER A 413 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 499 through 502 Processing sheet with id= G, first strand: chain 'A' and resid 707 through 709 removed outlier: 6.822A pdb=" N VAL A 944 " --> pdb=" O THR A 931 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU A 933 " --> pdb=" O ILE A 942 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE A 942 " --> pdb=" O LEU A 933 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 923 through 930 removed outlier: 4.738A pdb=" N LYS A 923 " --> pdb=" O ALA A 719 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL A 715 " --> pdb=" O GLU A 927 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR A 929 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 713 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR A 884 " --> pdb=" O PHE A 891 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 893 " --> pdb=" O ILE A 882 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ILE A 882 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ARG A 895 " --> pdb=" O MET A 880 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N MET A 880 " --> pdb=" O ARG A 895 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 752 through 757 Processing sheet with id= J, first strand: chain 'A' and resid 1033 through 1036 Processing sheet with id= K, first strand: chain 'B' and resid 88 through 90 removed outlier: 6.815A pdb=" N TRP B 141 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL B 123 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG B 139 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU B 125 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 137 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE B 127 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR B 135 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.602A pdb=" N GLN B 76 " --> pdb=" O VAL B 312 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 141 through 143 Processing sheet with id= N, first strand: chain 'B' and resid 265 through 269 426 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 4.66 Time building geometry restraints manager: 5.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.37: 3805 1.37 - 1.53: 5681 1.53 - 1.69: 2343 1.69 - 1.85: 71 1.85 - 2.01: 2 Bond restraints: 11902 Sorted by residual: bond pdb=" C2' AS C 22 " pdb=" C3' AS C 22 " ideal model delta sigma weight residual 1.222 1.528 -0.306 2.00e-02 2.50e+03 2.34e+02 bond pdb=" C2' AS C 23 " pdb=" C3' AS C 23 " ideal model delta sigma weight residual 1.222 1.525 -0.303 2.00e-02 2.50e+03 2.29e+02 bond pdb=" C4' AS C 23 " pdb=" O4' AS C 23 " ideal model delta sigma weight residual 1.267 1.445 -0.178 2.00e-02 2.50e+03 7.94e+01 bond pdb=" C4' AS C 22 " pdb=" O4' AS C 22 " ideal model delta sigma weight residual 1.267 1.444 -0.177 2.00e-02 2.50e+03 7.86e+01 bond pdb=" OP1 AS C 23 " pdb=" P AS C 23 " ideal model delta sigma weight residual 1.649 1.504 0.145 2.00e-02 2.50e+03 5.22e+01 ... (remaining 11897 not shown) Histogram of bond angle deviations from ideal: 92.39 - 100.95: 29 100.95 - 109.50: 1971 109.50 - 118.06: 7172 118.06 - 126.61: 6945 126.61 - 135.17: 245 Bond angle restraints: 16362 Sorted by residual: angle pdb=" C4' DC C 21 " pdb=" C3' DC C 21 " pdb=" O3' DC C 21 " ideal model delta sigma weight residual 110.00 120.66 -10.66 1.50e+00 4.44e-01 5.05e+01 angle pdb=" CA ASP A 886 " pdb=" CB ASP A 886 " pdb=" CG ASP A 886 " ideal model delta sigma weight residual 112.60 119.44 -6.84 1.00e+00 1.00e+00 4.68e+01 angle pdb=" CA ASP B 195 " pdb=" CB ASP B 195 " pdb=" CG ASP B 195 " ideal model delta sigma weight residual 112.60 118.70 -6.10 1.00e+00 1.00e+00 3.72e+01 angle pdb=" CA PHE A 891 " pdb=" CB PHE A 891 " pdb=" CG PHE A 891 " ideal model delta sigma weight residual 113.80 119.79 -5.99 1.00e+00 1.00e+00 3.59e+01 angle pdb=" O5' AS C 22 " pdb=" P AS C 22 " pdb=" OP1 AS C 22 " ideal model delta sigma weight residual 109.47 92.39 17.08 3.00e+00 1.11e-01 3.24e+01 ... (remaining 16357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 6259 17.58 - 35.15: 433 35.15 - 52.73: 195 52.73 - 70.31: 61 70.31 - 87.88: 11 Dihedral angle restraints: 6959 sinusoidal: 3078 harmonic: 3881 Sorted by residual: dihedral pdb=" CA PRO B 317 " pdb=" C PRO B 317 " pdb=" N GLN B 318 " pdb=" CA GLN B 318 " ideal model delta harmonic sigma weight residual -180.00 -152.06 -27.94 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA LEU A 390 " pdb=" C LEU A 390 " pdb=" N VAL A 391 " pdb=" CA VAL A 391 " ideal model delta harmonic sigma weight residual 180.00 153.40 26.60 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA ASP B 271 " pdb=" C ASP B 271 " pdb=" N CYS B 272 " pdb=" CA CYS B 272 " ideal model delta harmonic sigma weight residual -180.00 -154.51 -25.49 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 6956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1642 0.133 - 0.267: 195 0.267 - 0.400: 5 0.400 - 0.533: 0 0.533 - 0.666: 2 Chirality restraints: 1844 Sorted by residual: chirality pdb=" P DG C -2 " pdb=" OP1 DG C -2 " pdb=" OP2 DG C -2 " pdb=" O5' DG C -2 " both_signs ideal model delta sigma weight residual True 2.35 -3.01 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" P DG D 1 " pdb=" OP1 DG D 1 " pdb=" OP2 DG D 1 " pdb=" O5' DG D 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.63 2.00e-01 2.50e+01 9.98e+00 chirality pdb=" CA ASP A 284 " pdb=" N ASP A 284 " pdb=" C ASP A 284 " pdb=" CB ASP A 284 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 1841 not shown) Planarity restraints: 1937 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' AS C 23 " 0.223 2.00e-02 2.50e+03 5.42e-01 5.88e+03 pdb=" C2' AS C 23 " -0.952 2.00e-02 2.50e+03 pdb=" C3' AS C 23 " -0.385 2.00e-02 2.50e+03 pdb=" C4' AS C 23 " 0.361 2.00e-02 2.50e+03 pdb=" C5' AS C 23 " -0.468 2.00e-02 2.50e+03 pdb=" N9 AS C 23 " -0.090 2.00e-02 2.50e+03 pdb=" O3' AS C 23 " 0.528 2.00e-02 2.50e+03 pdb=" O4' AS C 23 " 0.782 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' AS C 22 " 0.373 2.00e-02 2.50e+03 2.73e-01 1.49e+03 pdb=" C2' AS C 22 " -0.217 2.00e-02 2.50e+03 pdb=" C3' AS C 22 " -0.386 2.00e-02 2.50e+03 pdb=" C4' AS C 22 " 0.294 2.00e-02 2.50e+03 pdb=" C5' AS C 22 " -0.244 2.00e-02 2.50e+03 pdb=" N9 AS C 22 " -0.187 2.00e-02 2.50e+03 pdb=" O3' AS C 22 " 0.256 2.00e-02 2.50e+03 pdb=" O4' AS C 22 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT D 4 " -0.120 2.00e-02 2.50e+03 5.63e-02 7.92e+01 pdb=" N1 DT D 4 " 0.025 2.00e-02 2.50e+03 pdb=" C2 DT D 4 " 0.019 2.00e-02 2.50e+03 pdb=" O2 DT D 4 " 0.074 2.00e-02 2.50e+03 pdb=" N3 DT D 4 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DT D 4 " -0.019 2.00e-02 2.50e+03 pdb=" O4 DT D 4 " -0.079 2.00e-02 2.50e+03 pdb=" C5 DT D 4 " 0.028 2.00e-02 2.50e+03 pdb=" C7 DT D 4 " 0.037 2.00e-02 2.50e+03 pdb=" C6 DT D 4 " 0.043 2.00e-02 2.50e+03 ... (remaining 1934 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.05: 1 2.05 - 2.76: 755 2.76 - 3.47: 15707 3.47 - 4.19: 29342 4.19 - 4.90: 48946 Nonbonded interactions: 94751 Sorted by model distance: nonbonded pdb=" OH ATYR A 577 " pdb=" O AHOH A1401 " model vdw 1.333 2.440 nonbonded pdb=" O VAL A 573 " pdb=" CD2BTYR A 577 " model vdw 2.143 3.340 nonbonded pdb=" OD1 ASP A 368 " pdb="CA CA A1302 " model vdw 2.154 2.510 nonbonded pdb=" NH2 ARG A1224 " pdb=" OD2 ASP B 63 " model vdw 2.189 2.520 nonbonded pdb=" NE ARG A1062 " pdb=" OE1 GLN A1064 " model vdw 2.257 2.520 ... (remaining 94746 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 5.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 21.790 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 44.860 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 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:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 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 : 0.011 0.306 11902 Z= 0.672 Angle : 1.431 17.078 16362 Z= 0.921 Chirality : 0.085 0.666 1844 Planarity : 0.019 0.542 1937 Dihedral : 15.615 87.882 4463 Min Nonbonded Distance : 1.333 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.36 % Allowed : 2.96 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.53 (0.22), residues: 1332 helix: -0.69 (0.22), residues: 466 sheet: 0.23 (0.30), residues: 259 loop : -0.13 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.009 TRP A 472 HIS 0.028 0.004 HIS A 729 PHE 0.034 0.007 PHE A 122 TYR 0.039 0.009 TYR A 206 ARG 0.029 0.003 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 185 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.7949 (pm20) cc_final: 0.7657 (pp20) REVERT: A 72 ASP cc_start: 0.7791 (p0) cc_final: 0.7126 (m-30) REVERT: A 73 GLU cc_start: 0.7520 (pp20) cc_final: 0.7294 (pm20) REVERT: A 91 ARG cc_start: 0.6658 (mtm-85) cc_final: 0.6106 (mtp85) REVERT: A 100 LYS cc_start: 0.7722 (mttp) cc_final: 0.7440 (mtmm) REVERT: A 162 MET cc_start: 0.7475 (mmm) cc_final: 0.7258 (mmp) REVERT: A 264 ARG cc_start: 0.7964 (mmm160) cc_final: 0.7547 (mmp-170) REVERT: A 358 ASP cc_start: 0.7408 (m-30) cc_final: 0.7004 (p0) REVERT: A 421 GLU cc_start: 0.7536 (tt0) cc_final: 0.7213 (mm-30) REVERT: A 500 ARG cc_start: 0.8227 (ttp-170) cc_final: 0.8009 (ttp80) REVERT: A 541 ASN cc_start: 0.7079 (m-40) cc_final: 0.6740 (p0) REVERT: A 559 ASP cc_start: 0.7135 (m-30) cc_final: 0.6914 (m-30) REVERT: A 597 GLU cc_start: 0.8207 (pt0) cc_final: 0.7547 (tp30) REVERT: A 617 GLN cc_start: 0.8474 (mt0) cc_final: 0.7492 (pp30) REVERT: A 630 ASP cc_start: 0.8260 (t70) cc_final: 0.7928 (m-30) REVERT: A 760 ARG cc_start: 0.7455 (mtp180) cc_final: 0.7041 (tpp80) REVERT: A 811 LYS cc_start: 0.8657 (ttpp) cc_final: 0.8432 (ttpp) REVERT: A 824 GLN cc_start: 0.7574 (tt0) cc_final: 0.7320 (tp40) REVERT: A 843 GLU cc_start: 0.7864 (tp30) cc_final: 0.7520 (mp0) REVERT: A 846 LEU cc_start: 0.8552 (mt) cc_final: 0.8350 (mt) REVERT: A 850 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8103 (mm-30) REVERT: A 912 HIS cc_start: 0.7722 (t70) cc_final: 0.7364 (t-170) REVERT: A 949 LYS cc_start: 0.8238 (tttp) cc_final: 0.7935 (tttm) REVERT: A 950 MET cc_start: 0.7989 (ttm) cc_final: 0.7686 (tpp) REVERT: A 1194 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6298 (pm20) REVERT: A 1196 TRP cc_start: 0.5129 (t60) cc_final: 0.4879 (t60) REVERT: B 32 GLN cc_start: 0.4988 (tt0) cc_final: 0.4422 (mt0) REVERT: B 85 GLN cc_start: 0.4818 (mt0) cc_final: 0.4464 (mm110) REVERT: B 117 TYR cc_start: 0.4276 (m-80) cc_final: 0.3843 (m-80) REVERT: B 125 LEU cc_start: 0.5345 (mt) cc_final: 0.5126 (mm) outliers start: 3 outliers final: 1 residues processed: 187 average time/residue: 1.4172 time to fit residues: 283.9281 Evaluate side-chains 136 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 921 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 35 optimal weight: 0.2980 chunk 70 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 107 optimal weight: 0.1980 chunk 41 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN ** A 580 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A 962 ASN A1179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11902 Z= 0.207 Angle : 0.737 17.987 16362 Z= 0.363 Chirality : 0.045 0.168 1844 Planarity : 0.005 0.040 1937 Dihedral : 17.203 78.501 2012 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.62 % Allowed : 6.91 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.22), residues: 1332 helix: 0.61 (0.24), residues: 476 sheet: 0.15 (0.29), residues: 275 loop : 0.23 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 130 HIS 0.009 0.001 HIS A 98 PHE 0.017 0.002 PHE A 444 TYR 0.019 0.002 TYR A 399 ARG 0.006 0.001 ARG B 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.6836 (OUTLIER) cc_final: 0.6627 (mt0) REVERT: A 70 GLU cc_start: 0.7930 (pm20) cc_final: 0.7541 (pp20) REVERT: A 73 GLU cc_start: 0.7555 (pp20) cc_final: 0.7215 (pm20) REVERT: A 91 ARG cc_start: 0.6628 (mtm-85) cc_final: 0.6143 (mtp85) REVERT: A 100 LYS cc_start: 0.7606 (mttp) cc_final: 0.7344 (mtmm) REVERT: A 264 ARG cc_start: 0.8030 (mmm160) cc_final: 0.7568 (mmp-170) REVERT: A 358 ASP cc_start: 0.7522 (m-30) cc_final: 0.7041 (p0) REVERT: A 421 GLU cc_start: 0.7406 (tt0) cc_final: 0.7081 (mm-30) REVERT: A 541 ASN cc_start: 0.6853 (m-40) cc_final: 0.6518 (p0) REVERT: A 559 ASP cc_start: 0.7143 (m-30) cc_final: 0.6913 (m-30) REVERT: A 597 GLU cc_start: 0.8245 (pt0) cc_final: 0.7489 (tp30) REVERT: A 617 GLN cc_start: 0.8554 (mt0) cc_final: 0.7521 (pp30) REVERT: A 630 ASP cc_start: 0.8467 (t70) cc_final: 0.7968 (m-30) REVERT: A 717 ASP cc_start: 0.8050 (t70) cc_final: 0.7606 (p0) REVERT: A 750 LYS cc_start: 0.8222 (tmmt) cc_final: 0.7958 (tmmt) REVERT: A 760 ARG cc_start: 0.7245 (mtp180) cc_final: 0.6970 (tpp80) REVERT: A 787 GLN cc_start: 0.7810 (tm-30) cc_final: 0.7485 (tm-30) REVERT: A 811 LYS cc_start: 0.8557 (ttpp) cc_final: 0.8053 (tppt) REVERT: A 824 GLN cc_start: 0.7695 (tt0) cc_final: 0.7412 (tp40) REVERT: A 843 GLU cc_start: 0.7802 (tp30) cc_final: 0.7444 (mp0) REVERT: A 846 LEU cc_start: 0.8368 (mt) cc_final: 0.8030 (mm) REVERT: A 850 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7806 (mm-30) REVERT: A 949 LYS cc_start: 0.8330 (tttp) cc_final: 0.8031 (tttm) REVERT: A 1194 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6250 (pm20) REVERT: A 1196 TRP cc_start: 0.5506 (t60) cc_final: 0.5186 (t60) REVERT: B 221 PHE cc_start: 0.2723 (m-80) cc_final: 0.2470 (m-80) outliers start: 17 outliers final: 7 residues processed: 149 average time/residue: 1.4213 time to fit residues: 227.9707 Evaluate side-chains 131 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 267 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 124 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN ** A 580 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11902 Z= 0.277 Angle : 0.774 17.573 16362 Z= 0.384 Chirality : 0.048 0.186 1844 Planarity : 0.006 0.078 1937 Dihedral : 17.289 71.149 2009 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.06 % Allowed : 8.26 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.23), residues: 1332 helix: 0.63 (0.24), residues: 473 sheet: 0.07 (0.29), residues: 274 loop : 0.37 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 130 HIS 0.011 0.002 HIS A 98 PHE 0.022 0.002 PHE A 590 TYR 0.023 0.002 TYR A 399 ARG 0.020 0.001 ARG A 873 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.7981 (pm20) cc_final: 0.7544 (pp20) REVERT: A 72 ASP cc_start: 0.7635 (p0) cc_final: 0.7146 (m-30) REVERT: A 73 GLU cc_start: 0.7542 (pp20) cc_final: 0.7201 (pm20) REVERT: A 91 ARG cc_start: 0.6622 (mtm-85) cc_final: 0.6195 (mtp-110) REVERT: A 100 LYS cc_start: 0.7589 (mttp) cc_final: 0.7341 (mtmm) REVERT: A 160 TYR cc_start: 0.7862 (t80) cc_final: 0.7643 (t80) REVERT: A 264 ARG cc_start: 0.8021 (mmm160) cc_final: 0.7530 (mmp-170) REVERT: A 421 GLU cc_start: 0.7378 (tt0) cc_final: 0.6999 (mm-30) REVERT: A 545 GLU cc_start: 0.6744 (mt-10) cc_final: 0.6303 (mm-30) REVERT: A 559 ASP cc_start: 0.7043 (m-30) cc_final: 0.6810 (m-30) REVERT: A 597 GLU cc_start: 0.8340 (pt0) cc_final: 0.7574 (tp30) REVERT: A 617 GLN cc_start: 0.8582 (mt0) cc_final: 0.7624 (pp30) REVERT: A 630 ASP cc_start: 0.8422 (t70) cc_final: 0.8003 (m-30) REVERT: A 717 ASP cc_start: 0.7874 (t70) cc_final: 0.7529 (p0) REVERT: A 750 LYS cc_start: 0.8218 (tmmt) cc_final: 0.8010 (tmmt) REVERT: A 760 ARG cc_start: 0.7193 (mtp180) cc_final: 0.6887 (tpp80) REVERT: A 787 GLN cc_start: 0.7805 (tm-30) cc_final: 0.7565 (tm-30) REVERT: A 824 GLN cc_start: 0.7748 (tt0) cc_final: 0.7417 (tp40) REVERT: A 843 GLU cc_start: 0.7799 (tp30) cc_final: 0.7397 (mp0) REVERT: A 846 LEU cc_start: 0.8341 (mt) cc_final: 0.8066 (mm) REVERT: A 850 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7887 (mm-30) REVERT: A 949 LYS cc_start: 0.8336 (tttp) cc_final: 0.8071 (tttm) REVERT: A 992 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7238 (pt0) REVERT: A 1196 TRP cc_start: 0.5704 (t60) cc_final: 0.5315 (t60) REVERT: B 124 GLU cc_start: 0.5662 (mt-10) cc_final: 0.5452 (tt0) REVERT: B 209 LYS cc_start: 0.5606 (tppt) cc_final: 0.5333 (tmtt) REVERT: B 221 PHE cc_start: 0.2746 (m-80) cc_final: 0.2204 (m-80) outliers start: 22 outliers final: 9 residues processed: 143 average time/residue: 1.3660 time to fit residues: 210.0592 Evaluate side-chains 131 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 304 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 125 optimal weight: 0.3980 chunk 132 optimal weight: 3.9990 chunk 65 optimal weight: 0.0980 chunk 118 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN A 466 ASN A 912 HIS B 32 GLN B 70 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11902 Z= 0.224 Angle : 0.696 15.996 16362 Z= 0.337 Chirality : 0.043 0.147 1844 Planarity : 0.005 0.047 1937 Dihedral : 17.259 75.226 2009 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.62 % Allowed : 9.78 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.57 (0.23), residues: 1332 helix: 0.92 (0.24), residues: 474 sheet: -0.02 (0.29), residues: 273 loop : 0.31 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 130 HIS 0.009 0.001 HIS A 98 PHE 0.015 0.002 PHE A 440 TYR 0.021 0.002 TYR A 399 ARG 0.007 0.001 ARG B 275 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 1.227 Fit side-chains revert: symmetry clash REVERT: A 63 GLN cc_start: 0.6776 (OUTLIER) cc_final: 0.4749 (pm20) REVERT: A 70 GLU cc_start: 0.7964 (pm20) cc_final: 0.7534 (pp20) REVERT: A 72 ASP cc_start: 0.7611 (p0) cc_final: 0.7208 (m-30) REVERT: A 73 GLU cc_start: 0.7608 (pp20) cc_final: 0.7250 (pm20) REVERT: A 91 ARG cc_start: 0.6617 (mtm-85) cc_final: 0.6193 (mtp-110) REVERT: A 100 LYS cc_start: 0.7584 (mttp) cc_final: 0.7343 (mtmm) REVERT: A 163 ARG cc_start: 0.7805 (ptt-90) cc_final: 0.7537 (ptt-90) REVERT: A 264 ARG cc_start: 0.8040 (mmm160) cc_final: 0.7583 (mmp-170) REVERT: A 421 GLU cc_start: 0.7403 (tt0) cc_final: 0.7012 (mm-30) REVERT: A 545 GLU cc_start: 0.6807 (mt-10) cc_final: 0.6274 (pt0) REVERT: A 559 ASP cc_start: 0.7057 (m-30) cc_final: 0.6849 (m-30) REVERT: A 597 GLU cc_start: 0.8288 (pt0) cc_final: 0.7520 (tp30) REVERT: A 617 GLN cc_start: 0.8591 (mt0) cc_final: 0.7660 (pp30) REVERT: A 630 ASP cc_start: 0.8450 (t70) cc_final: 0.7956 (m-30) REVERT: A 717 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7553 (p0) REVERT: A 750 LYS cc_start: 0.8197 (tmmt) cc_final: 0.7982 (tmmt) REVERT: A 760 ARG cc_start: 0.7156 (mtp180) cc_final: 0.6920 (ttm-80) REVERT: A 824 GLN cc_start: 0.7692 (tt0) cc_final: 0.7362 (tp40) REVERT: A 843 GLU cc_start: 0.7808 (tp30) cc_final: 0.7414 (mp0) REVERT: A 846 LEU cc_start: 0.8341 (mt) cc_final: 0.8054 (mm) REVERT: A 850 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7857 (mm-30) REVERT: A 949 LYS cc_start: 0.8313 (tttp) cc_final: 0.8063 (tttm) REVERT: A 992 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7321 (pt0) REVERT: A 1196 TRP cc_start: 0.5616 (t60) cc_final: 0.5248 (t60) REVERT: B 124 GLU cc_start: 0.5655 (mt-10) cc_final: 0.5443 (tt0) REVERT: B 209 LYS cc_start: 0.5474 (tppt) cc_final: 0.5248 (tptp) outliers start: 17 outliers final: 10 residues processed: 129 average time/residue: 1.3054 time to fit residues: 182.0178 Evaluate side-chains 126 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain B residue 304 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 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 323 ASN A 541 ASN A 912 HIS B 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11902 Z= 0.274 Angle : 0.727 15.760 16362 Z= 0.355 Chirality : 0.045 0.153 1844 Planarity : 0.005 0.052 1937 Dihedral : 17.332 72.804 2009 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.24 % Allowed : 9.34 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.46 (0.23), residues: 1332 helix: 0.83 (0.24), residues: 472 sheet: -0.22 (0.28), residues: 283 loop : 0.35 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 130 HIS 0.009 0.002 HIS A 729 PHE 0.020 0.002 PHE A 590 TYR 0.023 0.002 TYR A 399 ARG 0.008 0.001 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.320 Fit side-chains revert: symmetry clash REVERT: A 63 GLN cc_start: 0.6755 (OUTLIER) cc_final: 0.4732 (pm20) REVERT: A 70 GLU cc_start: 0.7980 (pm20) cc_final: 0.7548 (pp20) REVERT: A 72 ASP cc_start: 0.7611 (p0) cc_final: 0.7234 (m-30) REVERT: A 73 GLU cc_start: 0.7562 (pp20) cc_final: 0.7241 (pm20) REVERT: A 91 ARG cc_start: 0.6664 (mtm-85) cc_final: 0.6264 (mtp-110) REVERT: A 100 LYS cc_start: 0.7619 (mttp) cc_final: 0.7369 (mtmm) REVERT: A 264 ARG cc_start: 0.8033 (mmm160) cc_final: 0.7568 (mmp-170) REVERT: A 421 GLU cc_start: 0.7413 (tt0) cc_final: 0.7020 (mm-30) REVERT: A 545 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6341 (pt0) REVERT: A 559 ASP cc_start: 0.7055 (m-30) cc_final: 0.6834 (m-30) REVERT: A 597 GLU cc_start: 0.8318 (pt0) cc_final: 0.7544 (tp30) REVERT: A 617 GLN cc_start: 0.8591 (mt0) cc_final: 0.7681 (pp30) REVERT: A 630 ASP cc_start: 0.8392 (t70) cc_final: 0.7954 (m-30) REVERT: A 717 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7577 (p0) REVERT: A 750 LYS cc_start: 0.8192 (tmmt) cc_final: 0.7962 (tmmt) REVERT: A 760 ARG cc_start: 0.7173 (mtp180) cc_final: 0.6911 (ttm-80) REVERT: A 824 GLN cc_start: 0.7709 (tt0) cc_final: 0.7417 (tp40) REVERT: A 842 ARG cc_start: 0.8057 (mtm110) cc_final: 0.7731 (mtm-85) REVERT: A 843 GLU cc_start: 0.7787 (tp30) cc_final: 0.7386 (mp0) REVERT: A 846 LEU cc_start: 0.8310 (mt) cc_final: 0.7818 (mm) REVERT: A 850 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7881 (mm-30) REVERT: A 949 LYS cc_start: 0.8290 (tttp) cc_final: 0.8042 (tttm) REVERT: A 992 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7416 (pt0) REVERT: A 1052 LEU cc_start: 0.5373 (OUTLIER) cc_final: 0.5168 (mm) REVERT: B 124 GLU cc_start: 0.6008 (mt-10) cc_final: 0.5433 (tt0) outliers start: 24 outliers final: 13 residues processed: 141 average time/residue: 1.3811 time to fit residues: 209.7454 Evaluate side-chains 134 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 304 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 132 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN A 541 ASN A 912 HIS A1179 ASN B 70 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11902 Z= 0.237 Angle : 0.690 15.876 16362 Z= 0.335 Chirality : 0.043 0.144 1844 Planarity : 0.005 0.050 1937 Dihedral : 17.381 73.830 2009 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.33 % Allowed : 9.87 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.50 (0.23), residues: 1332 helix: 0.92 (0.24), residues: 473 sheet: -0.15 (0.28), residues: 276 loop : 0.27 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 130 HIS 0.009 0.001 HIS A 98 PHE 0.015 0.002 PHE A 590 TYR 0.022 0.002 TYR A 399 ARG 0.007 0.001 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 1.215 Fit side-chains REVERT: A 63 GLN cc_start: 0.6795 (OUTLIER) cc_final: 0.4759 (pm20) REVERT: A 70 GLU cc_start: 0.7977 (pm20) cc_final: 0.7546 (pp20) REVERT: A 72 ASP cc_start: 0.7594 (p0) cc_final: 0.7268 (m-30) REVERT: A 73 GLU cc_start: 0.7602 (pp20) cc_final: 0.7251 (pm20) REVERT: A 91 ARG cc_start: 0.6680 (mtm-85) cc_final: 0.6273 (mtp-110) REVERT: A 100 LYS cc_start: 0.7595 (mttp) cc_final: 0.7360 (mtmm) REVERT: A 264 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7578 (mmp-170) REVERT: A 274 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7618 (mpt-90) REVERT: A 421 GLU cc_start: 0.7411 (tt0) cc_final: 0.7017 (mm-30) REVERT: A 545 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6344 (pt0) REVERT: A 559 ASP cc_start: 0.7052 (m-30) cc_final: 0.6841 (m-30) REVERT: A 597 GLU cc_start: 0.8306 (pt0) cc_final: 0.7505 (tp30) REVERT: A 617 GLN cc_start: 0.8595 (mt0) cc_final: 0.7687 (pp30) REVERT: A 630 ASP cc_start: 0.8437 (t70) cc_final: 0.7933 (m-30) REVERT: A 717 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7583 (p0) REVERT: A 750 LYS cc_start: 0.8193 (tmmt) cc_final: 0.7930 (tmmt) REVERT: A 760 ARG cc_start: 0.7168 (mtp180) cc_final: 0.6893 (ttm-80) REVERT: A 824 GLN cc_start: 0.7671 (tt0) cc_final: 0.7311 (mm-40) REVERT: A 843 GLU cc_start: 0.7768 (tp30) cc_final: 0.7376 (mp0) REVERT: A 846 LEU cc_start: 0.8325 (mt) cc_final: 0.8035 (mm) REVERT: A 850 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7860 (mm-30) REVERT: A 949 LYS cc_start: 0.8309 (tttp) cc_final: 0.8070 (tttm) REVERT: A 1030 ASP cc_start: 0.7832 (t0) cc_final: 0.7578 (t0) REVERT: A 1042 ARG cc_start: 0.7366 (mtm180) cc_final: 0.6948 (mtp85) REVERT: B 124 GLU cc_start: 0.5928 (mt-10) cc_final: 0.5358 (tt0) REVERT: B 179 ARG cc_start: 0.5370 (mtm110) cc_final: 0.4912 (mtt-85) outliers start: 25 outliers final: 13 residues processed: 133 average time/residue: 1.3712 time to fit residues: 196.7071 Evaluate side-chains 128 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 304 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 96 optimal weight: 0.1980 chunk 74 optimal weight: 0.0670 chunk 111 optimal weight: 2.9990 chunk 132 optimal weight: 0.0050 chunk 82 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.2932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN A 541 ASN A 912 HIS B 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11902 Z= 0.152 Angle : 0.635 14.921 16362 Z= 0.303 Chirality : 0.040 0.139 1844 Planarity : 0.004 0.051 1937 Dihedral : 17.165 78.766 2009 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.80 % Allowed : 10.23 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.72 (0.23), residues: 1332 helix: 1.17 (0.24), residues: 474 sheet: -0.07 (0.28), residues: 276 loop : 0.36 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 141 HIS 0.005 0.001 HIS A 98 PHE 0.012 0.001 PHE A 444 TYR 0.019 0.001 TYR A 399 ARG 0.007 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 1.300 Fit side-chains REVERT: A 70 GLU cc_start: 0.7958 (pm20) cc_final: 0.7543 (pp20) REVERT: A 72 ASP cc_start: 0.7609 (p0) cc_final: 0.7261 (m-30) REVERT: A 73 GLU cc_start: 0.7585 (pp20) cc_final: 0.7250 (pm20) REVERT: A 91 ARG cc_start: 0.6706 (mtm-85) cc_final: 0.6281 (mtp-110) REVERT: A 100 LYS cc_start: 0.7574 (mttp) cc_final: 0.7334 (mtmm) REVERT: A 264 ARG cc_start: 0.8032 (mmm160) cc_final: 0.7583 (mmp-170) REVERT: A 274 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7447 (mpt-90) REVERT: A 421 GLU cc_start: 0.7399 (tt0) cc_final: 0.7006 (mm-30) REVERT: A 545 GLU cc_start: 0.6862 (mt-10) cc_final: 0.6312 (pt0) REVERT: A 597 GLU cc_start: 0.8270 (pt0) cc_final: 0.7477 (tp30) REVERT: A 617 GLN cc_start: 0.8572 (mt0) cc_final: 0.7661 (pp30) REVERT: A 630 ASP cc_start: 0.8344 (t70) cc_final: 0.7853 (m-30) REVERT: A 717 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7537 (p0) REVERT: A 750 LYS cc_start: 0.8188 (tmmt) cc_final: 0.7962 (tmmt) REVERT: A 824 GLN cc_start: 0.7662 (tt0) cc_final: 0.7298 (mm-40) REVERT: A 843 GLU cc_start: 0.7786 (tp30) cc_final: 0.7360 (mp0) REVERT: A 846 LEU cc_start: 0.8248 (mt) cc_final: 0.7719 (mm) REVERT: A 949 LYS cc_start: 0.8322 (tttp) cc_final: 0.8018 (tttm) REVERT: A 1030 ASP cc_start: 0.7844 (t0) cc_final: 0.7573 (t0) REVERT: A 1042 ARG cc_start: 0.7401 (mtm180) cc_final: 0.6949 (mtp85) REVERT: B 124 GLU cc_start: 0.5893 (mt-10) cc_final: 0.5319 (tt0) outliers start: 19 outliers final: 8 residues processed: 128 average time/residue: 1.3395 time to fit residues: 184.9188 Evaluate side-chains 125 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain B residue 269 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 120 optimal weight: 0.3980 chunk 126 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN A 541 ASN A 912 HIS B 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11902 Z= 0.212 Angle : 0.673 15.406 16362 Z= 0.324 Chirality : 0.042 0.143 1844 Planarity : 0.005 0.051 1937 Dihedral : 17.222 77.471 2009 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.53 % Allowed : 11.13 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.23), residues: 1332 helix: 1.08 (0.24), residues: 475 sheet: -0.18 (0.28), residues: 281 loop : 0.40 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 130 HIS 0.007 0.001 HIS A 98 PHE 0.016 0.002 PHE A 590 TYR 0.021 0.002 TYR A 399 ARG 0.007 0.001 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 1.163 Fit side-chains REVERT: A 70 GLU cc_start: 0.7983 (pm20) cc_final: 0.7558 (pp20) REVERT: A 72 ASP cc_start: 0.7578 (p0) cc_final: 0.7291 (m-30) REVERT: A 73 GLU cc_start: 0.7603 (pp20) cc_final: 0.7247 (pm20) REVERT: A 91 ARG cc_start: 0.6721 (mtm-85) cc_final: 0.6289 (mtp-110) REVERT: A 100 LYS cc_start: 0.7598 (mttp) cc_final: 0.7356 (mtmm) REVERT: A 264 ARG cc_start: 0.8042 (mmm160) cc_final: 0.7588 (mmp-170) REVERT: A 274 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7457 (mpt-90) REVERT: A 421 GLU cc_start: 0.7405 (tt0) cc_final: 0.7012 (mm-30) REVERT: A 545 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6356 (pt0) REVERT: A 597 GLU cc_start: 0.8296 (pt0) cc_final: 0.7501 (tp30) REVERT: A 617 GLN cc_start: 0.8612 (mt0) cc_final: 0.7688 (pp30) REVERT: A 630 ASP cc_start: 0.8319 (t70) cc_final: 0.7874 (m-30) REVERT: A 717 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7546 (p0) REVERT: A 750 LYS cc_start: 0.8169 (tmmt) cc_final: 0.7947 (tmmt) REVERT: A 824 GLN cc_start: 0.7656 (tt0) cc_final: 0.7291 (mm-40) REVERT: A 843 GLU cc_start: 0.7795 (tp30) cc_final: 0.7404 (mp0) REVERT: A 846 LEU cc_start: 0.8190 (mt) cc_final: 0.7988 (mm) REVERT: A 850 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7504 (mm-30) REVERT: A 949 LYS cc_start: 0.8319 (tttp) cc_final: 0.8012 (tttm) REVERT: A 1030 ASP cc_start: 0.7841 (t0) cc_final: 0.7561 (t0) REVERT: A 1042 ARG cc_start: 0.7454 (mtm180) cc_final: 0.6991 (mtp85) REVERT: B 124 GLU cc_start: 0.5901 (mt-10) cc_final: 0.5349 (tt0) outliers start: 16 outliers final: 11 residues processed: 123 average time/residue: 1.3438 time to fit residues: 178.3762 Evaluate side-chains 126 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain B residue 269 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 37 optimal weight: 0.2980 chunk 111 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN A 541 ASN A 912 HIS B 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11902 Z= 0.253 Angle : 0.702 15.808 16362 Z= 0.341 Chirality : 0.044 0.144 1844 Planarity : 0.005 0.054 1937 Dihedral : 17.298 73.773 2009 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.62 % Allowed : 11.31 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.50 (0.23), residues: 1332 helix: 0.95 (0.24), residues: 475 sheet: -0.28 (0.28), residues: 281 loop : 0.33 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 130 HIS 0.008 0.001 HIS A 98 PHE 0.017 0.002 PHE A 590 TYR 0.022 0.002 TYR A 399 ARG 0.007 0.001 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 1.250 Fit side-chains REVERT: A 70 GLU cc_start: 0.7993 (pm20) cc_final: 0.7560 (pp20) REVERT: A 72 ASP cc_start: 0.7572 (p0) cc_final: 0.7311 (m-30) REVERT: A 73 GLU cc_start: 0.7558 (pp20) cc_final: 0.7237 (pm20) REVERT: A 91 ARG cc_start: 0.6739 (mtm-85) cc_final: 0.6319 (mtp-110) REVERT: A 100 LYS cc_start: 0.7614 (mttp) cc_final: 0.7369 (mtmm) REVERT: A 264 ARG cc_start: 0.8035 (mmm160) cc_final: 0.7572 (mmp-170) REVERT: A 274 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7429 (mpt-90) REVERT: A 421 GLU cc_start: 0.7412 (tt0) cc_final: 0.7013 (mm-30) REVERT: A 545 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6362 (pt0) REVERT: A 597 GLU cc_start: 0.8309 (pt0) cc_final: 0.7517 (tp30) REVERT: A 617 GLN cc_start: 0.8607 (mt0) cc_final: 0.7688 (pp30) REVERT: A 630 ASP cc_start: 0.8325 (t70) cc_final: 0.7871 (m-30) REVERT: A 717 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7554 (p0) REVERT: A 750 LYS cc_start: 0.8185 (tmmt) cc_final: 0.7926 (tmmt) REVERT: A 824 GLN cc_start: 0.7700 (tt0) cc_final: 0.7344 (mm-40) REVERT: A 843 GLU cc_start: 0.7815 (tp30) cc_final: 0.7416 (mp0) REVERT: A 846 LEU cc_start: 0.8185 (mt) cc_final: 0.7760 (mm) REVERT: A 850 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7543 (mm-30) REVERT: A 949 LYS cc_start: 0.8295 (tttp) cc_final: 0.7989 (tttm) REVERT: A 1030 ASP cc_start: 0.7827 (t0) cc_final: 0.7542 (t0) REVERT: A 1042 ARG cc_start: 0.7428 (mtm180) cc_final: 0.6989 (mtp85) REVERT: B 90 ARG cc_start: 0.5049 (ttt180) cc_final: 0.4778 (tmt90) REVERT: B 124 GLU cc_start: 0.5973 (mt-10) cc_final: 0.5356 (tt0) outliers start: 17 outliers final: 12 residues processed: 124 average time/residue: 1.3300 time to fit residues: 178.7907 Evaluate side-chains 122 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 304 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 136 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN A 541 ASN A 912 HIS B 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11902 Z= 0.301 Angle : 0.734 16.214 16362 Z= 0.359 Chirality : 0.045 0.153 1844 Planarity : 0.005 0.055 1937 Dihedral : 17.468 68.199 2009 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.89 % Allowed : 11.22 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.43 (0.23), residues: 1332 helix: 0.88 (0.24), residues: 467 sheet: -0.35 (0.28), residues: 281 loop : 0.32 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 130 HIS 0.009 0.002 HIS A 729 PHE 0.020 0.002 PHE A 590 TYR 0.023 0.002 TYR A 399 ARG 0.008 0.001 ARG A 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.253 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.7996 (pm20) cc_final: 0.7567 (pp20) REVERT: A 72 ASP cc_start: 0.7566 (p0) cc_final: 0.7348 (m-30) REVERT: A 73 GLU cc_start: 0.7557 (pp20) cc_final: 0.7239 (pm20) REVERT: A 91 ARG cc_start: 0.6745 (mtm-85) cc_final: 0.6323 (mtp-110) REVERT: A 100 LYS cc_start: 0.7618 (mttp) cc_final: 0.7375 (mtmm) REVERT: A 264 ARG cc_start: 0.8035 (mmm160) cc_final: 0.7566 (mmp-170) REVERT: A 274 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7542 (mpt-90) REVERT: A 421 GLU cc_start: 0.7418 (tt0) cc_final: 0.7015 (mm-30) REVERT: A 545 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6384 (pt0) REVERT: A 597 GLU cc_start: 0.8319 (pt0) cc_final: 0.7525 (tp30) REVERT: A 617 GLN cc_start: 0.8601 (mt0) cc_final: 0.7702 (pp30) REVERT: A 630 ASP cc_start: 0.8347 (t70) cc_final: 0.7876 (m-30) REVERT: A 717 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7558 (p0) REVERT: A 750 LYS cc_start: 0.8179 (tmmt) cc_final: 0.7902 (tmmt) REVERT: A 824 GLN cc_start: 0.7692 (tt0) cc_final: 0.7346 (mm-40) REVERT: A 843 GLU cc_start: 0.7775 (tp30) cc_final: 0.7389 (mp0) REVERT: A 846 LEU cc_start: 0.8199 (mt) cc_final: 0.7773 (mm) REVERT: A 850 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7567 (mm-30) REVERT: A 1030 ASP cc_start: 0.7818 (t0) cc_final: 0.7516 (t0) REVERT: A 1042 ARG cc_start: 0.7384 (mtm180) cc_final: 0.6948 (mtp85) REVERT: A 1059 MET cc_start: 0.6353 (tmm) cc_final: 0.6054 (pp-130) REVERT: B 124 GLU cc_start: 0.5950 (mt-10) cc_final: 0.5351 (tt0) outliers start: 20 outliers final: 15 residues processed: 122 average time/residue: 1.2363 time to fit residues: 163.2567 Evaluate side-chains 127 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 304 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 111 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN A 541 ASN ** A 912 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.143462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.123475 restraints weight = 36659.811| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 3.18 r_work: 0.3115 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11902 Z= 0.221 Angle : 0.680 15.906 16362 Z= 0.328 Chirality : 0.042 0.143 1844 Planarity : 0.005 0.055 1937 Dihedral : 17.377 69.718 2009 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.71 % Allowed : 11.85 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.56 (0.23), residues: 1332 helix: 1.06 (0.24), residues: 469 sheet: -0.30 (0.28), residues: 280 loop : 0.34 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 130 HIS 0.008 0.001 HIS A 98 PHE 0.015 0.002 PHE A 590 TYR 0.022 0.002 TYR A 399 ARG 0.006 0.000 ARG A 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4738.70 seconds wall clock time: 83 minutes 14.71 seconds (4994.71 seconds total)