Starting phenix.real_space_refine on Sat Dec 9 22:13:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky5_23068/12_2023/7ky5_23068_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky5_23068/12_2023/7ky5_23068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky5_23068/12_2023/7ky5_23068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky5_23068/12_2023/7ky5_23068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky5_23068/12_2023/7ky5_23068_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky5_23068/12_2023/7ky5_23068_updated.pdb" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 62 5.16 5 C 8022 2.51 5 N 2053 2.21 5 O 2340 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 220": "OD1" <-> "OD2" Residue "A ASP 222": "OD1" <-> "OD2" Residue "A PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 592": "NH1" <-> "NH2" Residue "A ARG 627": "NH1" <-> "NH2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A TYR 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 746": "NH1" <-> "NH2" Residue "A GLU 763": "OE1" <-> "OE2" Residue "A ARG 768": "NH1" <-> "NH2" Residue "A GLU 828": "OE1" <-> "OE2" Residue "A ARG 854": "NH1" <-> "NH2" Residue "A ARG 891": "NH1" <-> "NH2" Residue "A ARG 893": "NH1" <-> "NH2" Residue "A ARG 959": "NH1" <-> "NH2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A ARG 996": "NH1" <-> "NH2" Residue "A GLU 997": "OE1" <-> "OE2" Residue "A GLU 1063": "OE1" <-> "OE2" Residue "A GLU 1066": "OE1" <-> "OE2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "A GLU 1096": "OE1" <-> "OE2" Residue "A ARG 1130": "NH1" <-> "NH2" Residue "A ARG 1131": "NH1" <-> "NH2" Residue "A ARG 1147": "NH1" <-> "NH2" Residue "A ARG 1196": "NH1" <-> "NH2" Residue "A ARG 1210": "NH1" <-> "NH2" Residue "A ARG 1214": "NH1" <-> "NH2" Residue "A PHE 1234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1300": "NH1" <-> "NH2" Residue "A ARG 1305": "NH1" <-> "NH2" Residue "A PHE 1313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1351": "NH1" <-> "NH2" Residue "A PHE 1371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1376": "NH1" <-> "NH2" Residue "A PHE 1408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1436": "NH1" <-> "NH2" Residue "A PHE 1437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1443": "NH1" <-> "NH2" Residue "A ARG 1455": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B ASP 202": "OD1" <-> "OD2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "B ASP 295": "OD1" <-> "OD2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 401": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12483 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1165, 9297 Classifications: {'peptide': 1165} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1125} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2974 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' MG': 1, 'ALF': 1, 'CLR': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 72 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.42, per 1000 atoms: 0.59 Number of scatterers: 12483 At special positions: 0 Unit cell: (133.812, 129.682, 137.942, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 62 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 2340 8.00 N 2053 7.00 C 8022 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied ALPHA1-4 " NAG C 2 " - " MAN C 3 " " NAG D 2 " - " MAN D 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG B 501 " - " ASN B 113 " " NAG B 502 " - " ASN B 256 " " NAG B 504 " - " ASN B 332 " " NAG C 1 " - " ASN B 240 " " NAG D 1 " - " ASN B 298 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.33 Conformation dependent library (CDL) restraints added in 2.2 seconds 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2882 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 10 sheets defined 40.3% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.52 Creating SS restraints... Processing helix chain 'A' and resid 245 through 253 Processing helix chain 'A' and resid 257 through 270 removed outlier: 3.994A pdb=" N ALA A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 311 Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 590 through 615 removed outlier: 4.482A pdb=" N ILE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL A 615 " --> pdb=" O THR A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 653 Processing helix chain 'A' and resid 660 through 679 removed outlier: 3.777A pdb=" N TYR A 663 " --> pdb=" O ILE A 660 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 664 " --> pdb=" O SER A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'A' and resid 702 through 705 Processing helix chain 'A' and resid 754 through 778 Processing helix chain 'A' and resid 795 through 800 Processing helix chain 'A' and resid 807 through 820 removed outlier: 3.612A pdb=" N ALA A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 855 Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 935 through 949 Processing helix chain 'A' and resid 963 through 976 Processing helix chain 'A' and resid 983 through 995 Processing helix chain 'A' and resid 1014 through 1023 Processing helix chain 'A' and resid 1036 through 1045 Processing helix chain 'A' and resid 1063 through 1067 removed outlier: 3.803A pdb=" N GLU A1066 " --> pdb=" O GLU A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1085 Processing helix chain 'A' and resid 1094 through 1101 Processing helix chain 'A' and resid 1117 through 1125 Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1177 through 1184 removed outlier: 4.577A pdb=" N GLN A1182 " --> pdb=" O ALA A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1237 removed outlier: 3.772A pdb=" N THR A1213 " --> pdb=" O PHE A1209 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG A1214 " --> pdb=" O ARG A1210 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A1217 " --> pdb=" O THR A1213 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY A1220 " --> pdb=" O VAL A1216 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS A1221 " --> pdb=" O LEU A1217 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A1228 " --> pdb=" O TYR A1224 " (cutoff:3.500A) Proline residue: A1232 - end of helix Processing helix chain 'A' and resid 1239 through 1250 removed outlier: 4.195A pdb=" N SER A1244 " --> pdb=" O ILE A1240 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A1245 " --> pdb=" O PHE A1241 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A1250 " --> pdb=" O PHE A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1271 removed outlier: 5.508A pdb=" N ASN A1269 " --> pdb=" O LEU A1265 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU A1270 " --> pdb=" O THR A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1275 through 1282 Processing helix chain 'A' and resid 1289 through 1294 Processing helix chain 'A' and resid 1296 through 1304 Processing helix chain 'A' and resid 1310 through 1336 Proline residue: A1331 - end of helix Processing helix chain 'A' and resid 1351 through 1373 Processing helix chain 'A' and resid 1381 through 1400 Processing helix chain 'A' and resid 1411 through 1415 Processing helix chain 'A' and resid 1419 through 1446 Proline residue: A1435 - end of helix removed outlier: 3.734A pdb=" N ILE A1445 " --> pdb=" O CYS A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1450 through 1460 Processing helix chain 'B' and resid 72 through 97 Proline residue: B 77 - end of helix Processing helix chain 'B' and resid 110 through 113 No H-bonds generated for 'chain 'B' and resid 110 through 113' Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 187 through 190 No H-bonds generated for 'chain 'B' and resid 187 through 190' Processing helix chain 'B' and resid 196 through 199 Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 233 through 236 No H-bonds generated for 'chain 'B' and resid 233 through 236' Processing helix chain 'B' and resid 268 through 272 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 373 through 397 Processing helix chain 'B' and resid 410 through 412 No H-bonds generated for 'chain 'B' and resid 410 through 412' Processing sheet with id= A, first strand: chain 'A' and resid 206 through 210 Processing sheet with id= B, first strand: chain 'A' and resid 451 through 455 removed outlier: 6.473A pdb=" N MET A 566 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU A 466 " --> pdb=" O MET A 566 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 490 through 493 removed outlier: 3.961A pdb=" N TYR A 477 " --> pdb=" O ARG A 558 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1028 through 1030 removed outlier: 7.216A pdb=" N TRP A1029 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE A 709 " --> pdb=" O TRP A1029 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N MET A1167 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE A 709 " --> pdb=" O MET A1167 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A1169 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N SER A 711 " --> pdb=" O LEU A1169 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 732 through 734 removed outlier: 3.861A pdb=" N LYS A 725 " --> pdb=" O ALA A1005 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA A1005 " --> pdb=" O LYS A 725 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N CYS A 727 " --> pdb=" O GLY A1003 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY A1003 " --> pdb=" O CYS A 727 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE A 729 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N LEU A1001 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU A 956 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY A1003 " --> pdb=" O LEU A 954 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU A 954 " --> pdb=" O GLY A1003 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ALA A1005 " --> pdb=" O ARG A 952 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ARG A 952 " --> pdb=" O ALA A1005 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LYS A 899 " --> pdb=" O VAL A 881 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N VAL A 881 " --> pdb=" O LYS A 899 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 875 through 878 removed outlier: 4.057A pdb=" N GLY A 867 " --> pdb=" O SER A 864 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 869 " --> pdb=" O GLY A 862 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLY A 862 " --> pdb=" O ILE A 869 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLU A 871 " --> pdb=" O PHE A 860 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N PHE A 860 " --> pdb=" O GLU A 871 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1054 through 1058 Processing sheet with id= H, first strand: chain 'A' and resid 1188 through 1190 removed outlier: 6.846A pdb=" N TYR A1204 " --> pdb=" O GLY A1189 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 126 through 129 removed outlier: 7.001A pdb=" N TYR B 177 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU B 326 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU B 179 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N THR B 324 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 141 through 145 481 hydrogen bonds defined for protein. 1308 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: 4.60 Time building geometry restraints manager: 5.72 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: 3934 1.34 - 1.46: 2193 1.46 - 1.58: 6540 1.58 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 12761 Sorted by residual: bond pdb=" F1 ALF A1703 " pdb="AL ALF A1703 " ideal model delta sigma weight residual 1.684 1.785 -0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" F3 ALF A1703 " pdb="AL ALF A1703 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" F4 ALF A1703 " pdb="AL ALF A1703 " ideal model delta sigma weight residual 1.686 1.786 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" F2 ALF A1703 " pdb="AL ALF A1703 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" C1 MAN C 3 " pdb=" C2 MAN C 3 " ideal model delta sigma weight residual 1.526 1.560 -0.034 2.00e-02 2.50e+03 2.90e+00 ... (remaining 12756 not shown) Histogram of bond angle deviations from ideal: 89.89 - 107.91: 461 107.91 - 125.92: 16667 125.92 - 143.94: 195 143.94 - 161.95: 0 161.95 - 179.96: 2 Bond angle restraints: 17325 Sorted by residual: angle pdb=" F1 ALF A1703 " pdb="AL ALF A1703 " pdb=" F2 ALF A1703 " ideal model delta sigma weight residual 108.68 179.91 -71.23 3.00e+00 1.11e-01 5.64e+02 angle pdb=" F3 ALF A1703 " pdb="AL ALF A1703 " pdb=" F4 ALF A1703 " ideal model delta sigma weight residual 109.63 179.96 -70.33 3.00e+00 1.11e-01 5.50e+02 angle pdb=" F2 ALF A1703 " pdb="AL ALF A1703 " pdb=" F4 ALF A1703 " ideal model delta sigma weight residual 110.21 90.14 20.07 3.00e+00 1.11e-01 4.48e+01 angle pdb=" F2 ALF A1703 " pdb="AL ALF A1703 " pdb=" F3 ALF A1703 " ideal model delta sigma weight residual 109.59 89.89 19.70 3.00e+00 1.11e-01 4.31e+01 angle pdb=" F1 ALF A1703 " pdb="AL ALF A1703 " pdb=" F3 ALF A1703 " ideal model delta sigma weight residual 109.69 90.07 19.62 3.00e+00 1.11e-01 4.28e+01 ... (remaining 17320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.41: 7279 21.41 - 42.82: 455 42.82 - 64.23: 42 64.23 - 85.63: 11 85.63 - 107.04: 9 Dihedral angle restraints: 7796 sinusoidal: 3317 harmonic: 4479 Sorted by residual: dihedral pdb=" CA ASN B 256 " pdb=" C ASN B 256 " pdb=" N TYR B 257 " pdb=" CA TYR B 257 " ideal model delta harmonic sigma weight residual -180.00 -158.26 -21.74 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA TYR A1335 " pdb=" C TYR A1335 " pdb=" N HIS A1336 " pdb=" CA HIS A1336 " ideal model delta harmonic sigma weight residual -180.00 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ASN A1252 " pdb=" C ASN A1252 " pdb=" N ASN A1253 " pdb=" CA ASN A1253 " ideal model delta harmonic sigma weight residual 180.00 159.86 20.14 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 7793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.176: 1963 0.176 - 0.352: 9 0.352 - 0.528: 1 0.528 - 0.704: 0 0.704 - 0.880: 1 Chirality restraints: 1974 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN B 240 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.28 0.88 2.00e-01 2.50e+01 1.94e+01 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 1.05e+01 chirality pdb=" C14 CLR A1701 " pdb=" C13 CLR A1701 " pdb=" C15 CLR A1701 " pdb=" C8 CLR A1701 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 1971 not shown) Planarity restraints: 2182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.314 2.00e-02 2.50e+03 2.65e-01 8.79e+02 pdb=" C7 NAG C 1 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.458 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 142 " 0.019 2.00e-02 2.50e+03 1.81e-02 8.15e+00 pdb=" CG TRP B 142 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP B 142 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B 142 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 142 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 142 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 142 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 142 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 142 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 142 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A1477 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO A1478 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A1478 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1478 " 0.035 5.00e-02 4.00e+02 ... (remaining 2179 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1147 2.74 - 3.28: 13463 3.28 - 3.82: 21275 3.82 - 4.36: 23987 4.36 - 4.90: 40139 Nonbonded interactions: 100011 Sorted by model distance: nonbonded pdb=" CD1 TYR A1409 " pdb=" NH2 ARG B 272 " model vdw 2.200 3.420 nonbonded pdb=" OG1 THR B 248 " pdb=" O GLN B 341 " model vdw 2.236 2.440 nonbonded pdb=" OG1 THR A 953 " pdb=" O THR A1004 " model vdw 2.240 2.440 nonbonded pdb=" OG1 THR A 718 " pdb=" O ARG A1009 " model vdw 2.263 2.440 nonbonded pdb=" O LEU A 703 " pdb=" OH TYR A1299 " model vdw 2.288 2.440 ... (remaining 100006 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 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 5.200 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 37.060 Find NCS groups from input model: 0.350 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 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 : 0.004 0.101 12761 Z= 0.234 Angle : 1.086 71.235 17325 Z= 0.477 Chirality : 0.052 0.880 1974 Planarity : 0.007 0.265 2177 Dihedral : 13.558 107.042 4908 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.07 % Allowed : 0.37 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.22), residues: 1520 helix: 0.59 (0.22), residues: 617 sheet: -0.47 (0.39), residues: 188 loop : -1.98 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP B 142 HIS 0.003 0.001 HIS A1350 PHE 0.039 0.002 PHE A1328 TYR 0.021 0.001 TYR A 260 ARG 0.011 0.001 ARG A1131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 0.2188 time to fit residues: 71.2919 Evaluate side-chains 159 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.430 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 0.0570 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 138 optimal weight: 0.0270 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 ASN A 873 GLN ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1323 GLN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12761 Z= 0.170 Angle : 0.803 29.913 17325 Z= 0.352 Chirality : 0.043 0.228 1974 Planarity : 0.004 0.048 2177 Dihedral : 8.887 94.220 1993 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.78 % Allowed : 9.95 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.22), residues: 1520 helix: 0.27 (0.21), residues: 625 sheet: -0.50 (0.39), residues: 188 loop : -1.96 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 142 HIS 0.002 0.001 HIS A 520 PHE 0.064 0.002 PHE B 395 TYR 0.021 0.001 TYR A1322 ARG 0.004 0.000 ARG A 625 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 187 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 18 residues processed: 193 average time/residue: 0.2067 time to fit residues: 62.9489 Evaluate side-chains 179 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 161 time to evaluate : 1.519 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1262 time to fit residues: 6.3272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 0.4980 chunk 42 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 123 optimal weight: 0.0570 chunk 137 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 overall best weight: 2.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12761 Z= 0.208 Angle : 0.793 29.792 17325 Z= 0.350 Chirality : 0.043 0.231 1974 Planarity : 0.004 0.050 2177 Dihedral : 8.530 91.529 1993 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.71 % Allowed : 13.81 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.22), residues: 1520 helix: 0.23 (0.21), residues: 613 sheet: -0.46 (0.38), residues: 198 loop : -1.95 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 348 HIS 0.003 0.001 HIS B 186 PHE 0.034 0.002 PHE B 395 TYR 0.023 0.002 TYR A1322 ARG 0.006 0.000 ARG A 625 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 164 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 176 average time/residue: 0.2048 time to fit residues: 56.9290 Evaluate side-chains 165 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 151 time to evaluate : 1.576 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1182 time to fit residues: 5.0316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.1980 chunk 103 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 15 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 ASN ** A1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 GLN ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12761 Z= 0.175 Angle : 0.777 30.009 17325 Z= 0.338 Chirality : 0.043 0.249 1974 Planarity : 0.004 0.051 2177 Dihedral : 8.264 86.461 1993 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.34 % Allowed : 15.74 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.22), residues: 1520 helix: 0.17 (0.21), residues: 616 sheet: -0.45 (0.38), residues: 198 loop : -1.90 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 562 HIS 0.002 0.001 HIS B 186 PHE 0.039 0.002 PHE B 395 TYR 0.016 0.001 TYR B 360 ARG 0.004 0.000 ARG A 625 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 167 average time/residue: 0.2113 time to fit residues: 55.1974 Evaluate side-chains 162 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 1.567 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1219 time to fit residues: 4.5232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 2 optimal weight: 0.0770 chunk 109 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 overall best weight: 3.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 GLN ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12761 Z= 0.263 Angle : 0.813 30.834 17325 Z= 0.365 Chirality : 0.044 0.229 1974 Planarity : 0.004 0.053 2177 Dihedral : 8.392 86.321 1993 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.67 % Allowed : 17.15 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.22), residues: 1520 helix: 0.05 (0.21), residues: 632 sheet: -0.53 (0.37), residues: 205 loop : -1.86 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 348 HIS 0.004 0.001 HIS B 186 PHE 0.035 0.002 PHE B 395 TYR 0.011 0.001 TYR A1322 ARG 0.007 0.000 ARG A 625 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 155 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 24 residues processed: 177 average time/residue: 0.2132 time to fit residues: 58.6612 Evaluate side-chains 166 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 1.494 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1198 time to fit residues: 7.4622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 147 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12761 Z= 0.155 Angle : 0.784 29.838 17325 Z= 0.341 Chirality : 0.043 0.284 1974 Planarity : 0.004 0.054 2177 Dihedral : 7.953 80.727 1993 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.82 % Allowed : 19.01 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.22), residues: 1520 helix: 0.21 (0.21), residues: 617 sheet: -0.35 (0.39), residues: 186 loop : -1.83 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 348 HIS 0.002 0.000 HIS B 186 PHE 0.046 0.002 PHE B 395 TYR 0.011 0.001 TYR A1322 ARG 0.003 0.000 ARG A 625 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 157 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 161 average time/residue: 0.2180 time to fit residues: 54.7563 Evaluate side-chains 153 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 147 time to evaluate : 1.335 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1145 time to fit residues: 3.0848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12761 Z= 0.164 Angle : 0.784 29.671 17325 Z= 0.340 Chirality : 0.043 0.270 1974 Planarity : 0.004 0.056 2177 Dihedral : 7.714 78.772 1993 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.19 % Allowed : 20.19 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.22), residues: 1520 helix: 0.21 (0.21), residues: 618 sheet: -0.26 (0.39), residues: 186 loop : -1.79 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1395 HIS 0.002 0.000 HIS B 186 PHE 0.030 0.002 PHE A1241 TYR 0.008 0.001 TYR A1322 ARG 0.004 0.000 ARG A 625 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 167 average time/residue: 0.1866 time to fit residues: 50.2068 Evaluate side-chains 154 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 1.390 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1590 time to fit residues: 4.7122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 13 optimal weight: 0.0870 chunk 115 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 140 optimal weight: 0.0470 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 ASN A 809 GLN ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12761 Z= 0.147 Angle : 0.803 29.519 17325 Z= 0.348 Chirality : 0.044 0.300 1974 Planarity : 0.004 0.057 2177 Dihedral : 7.325 74.275 1993 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.52 % Allowed : 20.42 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.22), residues: 1520 helix: 0.21 (0.21), residues: 607 sheet: -0.23 (0.39), residues: 186 loop : -1.76 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1395 HIS 0.002 0.000 HIS A1350 PHE 0.054 0.002 PHE A1241 TYR 0.023 0.001 TYR A 229 ARG 0.005 0.000 ARG A1300 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 163 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 165 average time/residue: 0.2039 time to fit residues: 54.0515 Evaluate side-chains 147 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 1.456 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1266 time to fit residues: 2.9904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 140 optimal weight: 0.0670 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 ASN A 809 GLN ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12761 Z= 0.208 Angle : 0.819 29.930 17325 Z= 0.360 Chirality : 0.044 0.289 1974 Planarity : 0.004 0.058 2177 Dihedral : 7.266 73.116 1993 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.74 % Allowed : 21.75 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.22), residues: 1520 helix: 0.22 (0.21), residues: 607 sheet: -0.33 (0.39), residues: 187 loop : -1.75 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A1395 HIS 0.003 0.001 HIS B 186 PHE 0.056 0.002 PHE B 395 TYR 0.011 0.001 TYR A 229 ARG 0.005 0.000 ARG A 625 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 146 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 151 average time/residue: 0.2077 time to fit residues: 49.6868 Evaluate side-chains 145 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 1.478 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1194 time to fit residues: 3.8000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 151 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 GLN ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 ASN ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12761 Z= 0.282 Angle : 0.875 30.601 17325 Z= 0.395 Chirality : 0.046 0.316 1974 Planarity : 0.004 0.057 2177 Dihedral : 7.313 70.460 1993 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 23.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.89 % Allowed : 21.83 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.21), residues: 1520 helix: 0.06 (0.21), residues: 611 sheet: -0.69 (0.37), residues: 198 loop : -1.80 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1395 HIS 0.003 0.001 HIS B 186 PHE 0.060 0.003 PHE B 395 TYR 0.011 0.002 TYR A1248 ARG 0.006 0.001 ARG A 625 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 147 average time/residue: 0.2266 time to fit residues: 53.6613 Evaluate side-chains 140 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 134 time to evaluate : 1.333 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1415 time to fit residues: 3.4659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 120 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.087958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.069924 restraints weight = 58499.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.071757 restraints weight = 35243.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.072729 restraints weight = 24292.900| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12761 Z= 0.214 Angle : 0.840 29.955 17325 Z= 0.371 Chirality : 0.045 0.319 1974 Planarity : 0.004 0.056 2177 Dihedral : 7.000 66.654 1993 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.67 % Allowed : 22.35 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.22), residues: 1520 helix: 0.12 (0.21), residues: 609 sheet: -0.56 (0.39), residues: 187 loop : -1.78 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1395 HIS 0.003 0.001 HIS B 186 PHE 0.052 0.002 PHE B 395 TYR 0.010 0.001 TYR A1268 ARG 0.004 0.000 ARG A 625 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2555.95 seconds wall clock time: 50 minutes 44.46 seconds (3044.46 seconds total)