Starting phenix.real_space_refine (version: dev) on Tue Feb 21 04:07:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npl_0473/02_2023/6npl_0473_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npl_0473/02_2023/6npl_0473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npl_0473/02_2023/6npl_0473.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npl_0473/02_2023/6npl_0473.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npl_0473/02_2023/6npl_0473_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npl_0473/02_2023/6npl_0473_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.010 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 Process input model Symmetric amino acids flipped Residue "A ARG 216": "NH1" <-> "NH2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A ASP 468": "OD1" <-> "OD2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 630": "NH1" <-> "NH2" Residue "A TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 726": "NH1" <-> "NH2" Residue "A GLU 759": "OE1" <-> "OE2" Residue "A ARG 769": "NH1" <-> "NH2" Residue "A ARG 803": "NH1" <-> "NH2" Residue "A PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 849": "OE1" <-> "OE2" Residue "A ARG 932": "NH1" <-> "NH2" Residue "A TYR 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 979": "NH1" <-> "NH2" Residue "A ARG 988": "NH1" <-> "NH2" Residue "A ARG 994": "NH1" <-> "NH2" Residue "A ARG 1004": "NH1" <-> "NH2" Residue "A PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1039": "OE1" <-> "OE2" Residue "A TYR 1066": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1072": "NH1" <-> "NH2" Residue "A ARG 1098": "NH1" <-> "NH2" Residue "A TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 404": "NH1" <-> "NH2" Residue "B ASP 468": "OD1" <-> "OD2" Residue "B PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 630": "NH1" <-> "NH2" Residue "B TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 726": "NH1" <-> "NH2" Residue "B ARG 769": "NH1" <-> "NH2" Residue "B ARG 803": "NH1" <-> "NH2" Residue "B PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 932": "NH1" <-> "NH2" Residue "B TYR 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 979": "NH1" <-> "NH2" Residue "B PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 988": "NH1" <-> "NH2" Residue "B ARG 994": "NH1" <-> "NH2" Residue "B PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1033": "OE1" <-> "OE2" Residue "B GLU 1039": "OE1" <-> "OE2" Residue "B GLU 1043": "OE1" <-> "OE2" Residue "B TYR 1066": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1072": "NH1" <-> "NH2" Residue "B ARG 1098": "NH1" <-> "NH2" Residue "B TYR 1107": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13774 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 861, 6702 Classifications: {'peptide': 861} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 834} Chain breaks: 1 Chain: "B" Number of atoms: 6702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 861, 6702 Classifications: {'peptide': 861} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 834} Chain breaks: 1 Chain: "A" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 159 Unusual residues: {' K': 1, ' CL': 2, 'POV': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 211 Unusual residues: {' K': 1, ' CL': 2, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 7.76, per 1000 atoms: 0.56 Number of scatterers: 13774 At special positions: 0 Unit cell: (118.16, 88.62, 161.415, 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) K 2 19.00 Cl 4 17.00 S 76 16.00 P 7 15.00 O 2448 8.00 N 2235 7.00 C 9002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 496 " - pdb=" SG CYS A 507 " distance=2.04 Simple disulfide: pdb=" SG CYS B 496 " - pdb=" SG CYS B 507 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.31 Conformation dependent library (CDL) restraints added in 2.1 seconds 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3172 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 3 sheets defined 50.1% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 209 through 221 removed outlier: 5.116A pdb=" N VAL A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ARG A 216 " --> pdb=" O GLY A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 236 Processing helix chain 'A' and resid 239 through 264 Processing helix chain 'A' and resid 274 through 281 removed outlier: 3.926A pdb=" N ILE A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 319 removed outlier: 4.038A pdb=" N SER A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 348 removed outlier: 3.868A pdb=" N ARG A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 374 removed outlier: 4.241A pdb=" N ALA A 354 " --> pdb=" O MET A 350 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR A 366 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 397 Processing helix chain 'A' and resid 412 through 418 Proline residue: A 417 - end of helix Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 435 through 462 Proline residue: A 440 - end of helix removed outlier: 3.599A pdb=" N LEU A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 521 Processing helix chain 'A' and resid 532 through 544 removed outlier: 3.842A pdb=" N LEU A 537 " --> pdb=" O PHE A 533 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 562 through 565 removed outlier: 4.429A pdb=" N ILE A 565 " --> pdb=" O GLY A 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 562 through 565' Processing helix chain 'A' and resid 577 through 591 Processing helix chain 'A' and resid 596 through 623 Proline residue: A 601 - end of helix Processing helix chain 'A' and resid 638 through 655 Processing helix chain 'A' and resid 657 through 675 removed outlier: 3.583A pdb=" N VAL A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 702 removed outlier: 3.926A pdb=" N HIS A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 699 " --> pdb=" O ALA A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 735 Processing helix chain 'A' and resid 760 through 773 Processing helix chain 'A' and resid 788 through 796 removed outlier: 3.979A pdb=" N TYR A 794 " --> pdb=" O GLN A 790 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET A 795 " --> pdb=" O GLY A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 835 removed outlier: 3.758A pdb=" N ASN A 830 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 832 " --> pdb=" O TYR A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 937 removed outlier: 3.855A pdb=" N GLN A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 968 Proline residue: A 964 - end of helix Processing helix chain 'A' and resid 992 through 1002 removed outlier: 3.841A pdb=" N LEU A 999 " --> pdb=" O ALA A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1029 removed outlier: 3.750A pdb=" N GLU A1027 " --> pdb=" O GLU A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1048 Processing helix chain 'A' and resid 1067 through 1083 Processing helix chain 'A' and resid 1104 through 1114 Processing helix chain 'B' and resid 209 through 221 removed outlier: 5.144A pdb=" N VAL B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ARG B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 239 through 264 Processing helix chain 'B' and resid 275 through 281 Processing helix chain 'B' and resid 284 through 319 removed outlier: 3.850A pdb=" N SER B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 348 removed outlier: 4.030A pdb=" N ARG B 332 " --> pdb=" O THR B 328 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY B 344 " --> pdb=" O ILE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 374 removed outlier: 4.171A pdb=" N ALA B 354 " --> pdb=" O MET B 350 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS B 355 " --> pdb=" O GLU B 351 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B 366 " --> pdb=" O VAL B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 398 Processing helix chain 'B' and resid 412 through 418 Proline residue: B 417 - end of helix Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 435 through 462 Proline residue: B 440 - end of helix removed outlier: 3.974A pdb=" N LEU B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 521 Processing helix chain 'B' and resid 532 through 556 removed outlier: 3.682A pdb=" N LEU B 537 " --> pdb=" O PHE B 533 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 539 " --> pdb=" O ALA B 535 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER B 546 " --> pdb=" O ALA B 542 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA B 547 " --> pdb=" O SER B 543 " (cutoff:3.500A) Proline residue: B 548 - end of helix Processing helix chain 'B' and resid 562 through 565 removed outlier: 4.347A pdb=" N ILE B 565 " --> pdb=" O GLY B 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 562 through 565' Processing helix chain 'B' and resid 577 through 591 removed outlier: 3.586A pdb=" N PHE B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 623 Proline residue: B 601 - end of helix Processing helix chain 'B' and resid 638 through 655 Processing helix chain 'B' and resid 657 through 675 removed outlier: 3.536A pdb=" N VAL B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 703 Processing helix chain 'B' and resid 727 through 735 Processing helix chain 'B' and resid 760 through 773 removed outlier: 3.607A pdb=" N ARG B 769 " --> pdb=" O LEU B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 796 removed outlier: 3.658A pdb=" N MET B 795 " --> pdb=" O GLY B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 838 removed outlier: 3.997A pdb=" N GLU B 826 " --> pdb=" O LYS B 823 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE B 829 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ASN B 830 " --> pdb=" O THR B 827 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS B 833 " --> pdb=" O ASN B 830 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE B 836 " --> pdb=" O HIS B 833 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP B 837 " --> pdb=" O ASP B 834 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE B 838 " --> pdb=" O ALA B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 936 removed outlier: 3.633A pdb=" N ASP B 935 " --> pdb=" O GLN B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 968 Proline residue: B 964 - end of helix Processing helix chain 'B' and resid 992 through 1002 removed outlier: 3.721A pdb=" N LEU B 999 " --> pdb=" O ALA B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1031 Processing helix chain 'B' and resid 1033 through 1035 No H-bonds generated for 'chain 'B' and resid 1033 through 1035' Processing helix chain 'B' and resid 1042 through 1051 removed outlier: 3.991A pdb=" N LEU B1050 " --> pdb=" O ALA B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1083 removed outlier: 3.816A pdb=" N GLU B1078 " --> pdb=" O ILE B1074 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1115 removed outlier: 3.614A pdb=" N THR B1113 " --> pdb=" O ALA B1109 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B1114 " --> pdb=" O TRP B1110 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER B1115 " --> pdb=" O LEU B1111 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 949 through 951 removed outlier: 3.509A pdb=" N ASP A 949 " --> pdb=" O LEU A1089 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER A1093 " --> pdb=" O TRP A 951 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N MET A1092 " --> pdb=" O PRO A1120 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU A1122 " --> pdb=" O MET A1092 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY A 812 " --> pdb=" O MET A 719 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 981 through 983 removed outlier: 6.253A pdb=" N THR A1011 " --> pdb=" O ILE A 982 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 1010 through 1013 removed outlier: 8.455A pdb=" N THR B1011 " --> pdb=" O ILE B 978 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL B 980 " --> pdb=" O THR B1011 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU B1013 " --> pdb=" O VAL B 980 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 982 " --> pdb=" O LEU B1013 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY B 983 " --> pdb=" O TRP B 952 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU B1089 " --> pdb=" O ASP B 949 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N TRP B 951 " --> pdb=" O LEU B1089 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL B1091 " --> pdb=" O TRP B 951 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B1121 " --> pdb=" O ARG B 846 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 846 " --> pdb=" O ILE B1121 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLY B 812 " --> pdb=" O MET B 719 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU B 742 " --> pdb=" O CYS B 716 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL B 718 " --> pdb=" O LEU B 742 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU B 744 " --> pdb=" O VAL B 718 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1707 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 5.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2141 1.31 - 1.44: 3806 1.44 - 1.57: 7952 1.57 - 1.70: 42 1.70 - 1.83: 120 Bond restraints: 14061 Sorted by residual: bond pdb=" C31 POV A1205 " pdb=" O31 POV A1205 " ideal model delta sigma weight residual 1.327 1.438 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C31 POV B1205 " pdb=" O31 POV B1205 " ideal model delta sigma weight residual 1.327 1.433 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C31 POV B1204 " pdb=" O31 POV B1204 " ideal model delta sigma weight residual 1.327 1.432 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C31 POV A1204 " pdb=" O31 POV A1204 " ideal model delta sigma weight residual 1.327 1.431 -0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C21 POV A1206 " pdb=" O21 POV A1206 " ideal model delta sigma weight residual 1.330 1.434 -0.104 2.00e-02 2.50e+03 2.68e+01 ... (remaining 14056 not shown) Histogram of bond angle deviations from ideal: 79.65 - 91.31: 4 91.31 - 102.97: 81 102.97 - 114.63: 8643 114.63 - 126.29: 10042 126.29 - 137.95: 229 Bond angle restraints: 18999 Sorted by residual: angle pdb=" C12 POV A1206 " pdb=" N POV A1206 " pdb=" C15 POV A1206 " ideal model delta sigma weight residual 112.10 80.90 31.20 3.00e+00 1.11e-01 1.08e+02 angle pdb=" C13 POV A1206 " pdb=" N POV A1206 " pdb=" C14 POV A1206 " ideal model delta sigma weight residual 108.80 79.65 29.15 3.00e+00 1.11e-01 9.44e+01 angle pdb=" C13 POV A1206 " pdb=" N POV A1206 " pdb=" C15 POV A1206 " ideal model delta sigma weight residual 109.35 80.50 28.85 3.00e+00 1.11e-01 9.25e+01 angle pdb=" C12 POV A1206 " pdb=" N POV A1206 " pdb=" C14 POV A1206 " ideal model delta sigma weight residual 107.13 80.33 26.80 3.00e+00 1.11e-01 7.98e+01 angle pdb=" C14 POV A1206 " pdb=" N POV A1206 " pdb=" C15 POV A1206 " ideal model delta sigma weight residual 108.02 132.28 -24.26 3.00e+00 1.11e-01 6.54e+01 ... (remaining 18994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.83: 7812 27.83 - 55.67: 426 55.67 - 83.50: 53 83.50 - 111.34: 8 111.34 - 139.17: 6 Dihedral angle restraints: 8305 sinusoidal: 3357 harmonic: 4948 Sorted by residual: dihedral pdb=" CA SER B 525 " pdb=" C SER B 525 " pdb=" N PRO B 526 " pdb=" CA PRO B 526 " ideal model delta harmonic sigma weight residual -180.00 -151.83 -28.17 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA SER A 525 " pdb=" C SER A 525 " pdb=" N PRO A 526 " pdb=" CA PRO A 526 " ideal model delta harmonic sigma weight residual -180.00 -152.64 -27.36 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA LEU B1037 " pdb=" C LEU B1037 " pdb=" N ARG B1038 " pdb=" CA ARG B1038 " ideal model delta harmonic sigma weight residual 180.00 153.69 26.31 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 8302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1716 0.064 - 0.128: 379 0.128 - 0.192: 38 0.192 - 0.256: 4 0.256 - 0.320: 2 Chirality restraints: 2139 Sorted by residual: chirality pdb=" CB VAL B 339 " pdb=" CA VAL B 339 " pdb=" CG1 VAL B 339 " pdb=" CG2 VAL B 339 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB VAL A 339 " pdb=" CA VAL A 339 " pdb=" CG1 VAL A 339 " pdb=" CG2 VAL A 339 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB ILE B1058 " pdb=" CA ILE B1058 " pdb=" CG1 ILE B1058 " pdb=" CG2 ILE B1058 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2136 not shown) Planarity restraints: 2349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B1119 " 0.054 5.00e-02 4.00e+02 8.17e-02 1.07e+01 pdb=" N PRO B1120 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO B1120 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B1120 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A1119 " 0.054 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO A1120 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A1120 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A1120 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 416 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO A 417 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 417 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 417 " 0.042 5.00e-02 4.00e+02 ... (remaining 2346 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.84: 4485 2.84 - 3.41: 13991 3.41 - 3.99: 25070 3.99 - 4.56: 35552 4.56 - 5.14: 52233 Nonbonded interactions: 131331 Sorted by model distance: nonbonded pdb=" O LEU A 771 " pdb=" OG SER A 776 " model vdw 2.264 2.440 nonbonded pdb=" O CYS A 496 " pdb=" OG SER A 505 " model vdw 2.294 2.440 nonbonded pdb=" OE1 GLN B 406 " pdb=" OG SER B 410 " model vdw 2.300 2.440 nonbonded pdb=" O GLU B 824 " pdb=" OG1 THR B 827 " model vdw 2.308 2.440 nonbonded pdb=" OD2 ASP A 391 " pdb=" OH TYR A 489 " model vdw 2.314 2.440 ... (remaining 131326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 206 through 1136 or resid 1201 through 1206)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 7 5.49 5 S 76 5.16 5 Cl 4 4.86 5 C 9002 2.51 5 N 2235 2.21 5 O 2448 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 3.490 Check model and map are aligned: 0.210 Process input model: 37.050 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.120 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:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 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 : 0.009 0.111 14061 Z= 0.557 Angle : 1.180 31.197 18999 Z= 0.541 Chirality : 0.053 0.320 2139 Planarity : 0.007 0.082 2349 Dihedral : 16.966 139.172 5127 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.46 % Favored : 91.48 % Rotamer Outliers : 7.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.62 (0.15), residues: 1714 helix: -2.57 (0.12), residues: 927 sheet: -2.45 (0.41), residues: 130 loop : -3.80 (0.18), residues: 657 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 358 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 19 residues processed: 437 average time/residue: 0.9027 time to fit residues: 444.4071 Evaluate side-chains 234 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 215 time to evaluate : 1.343 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 16 residues processed: 6 average time/residue: 0.1898 time to fit residues: 3.9261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN A 436 GLN A 573 ASN A 664 ASN A 739 ASN A 768 GLN A 797 GLN A 815 ASN A 833 HIS A1061 ASN B 266 ASN B 298 ASN B 327 GLN B 427 ASN B 436 GLN ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 701 GLN B 833 HIS B 938 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 14061 Z= 0.258 Angle : 0.847 35.951 18999 Z= 0.386 Chirality : 0.045 0.214 2139 Planarity : 0.005 0.077 2349 Dihedral : 13.986 119.246 2107 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer Outliers : 6.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.18), residues: 1714 helix: -0.80 (0.16), residues: 917 sheet: -1.65 (0.42), residues: 140 loop : -3.36 (0.20), residues: 657 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 256 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 31 residues processed: 318 average time/residue: 0.8718 time to fit residues: 314.4714 Evaluate side-chains 242 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 211 time to evaluate : 1.373 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 27 residues processed: 6 average time/residue: 0.1639 time to fit residues: 3.6045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 155 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 HIS ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1017 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 14061 Z= 0.240 Angle : 0.665 13.004 18999 Z= 0.325 Chirality : 0.045 0.405 2139 Planarity : 0.005 0.073 2349 Dihedral : 13.147 112.239 2107 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer Outliers : 6.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.20), residues: 1714 helix: -0.06 (0.17), residues: 922 sheet: -1.50 (0.42), residues: 137 loop : -3.18 (0.21), residues: 655 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 235 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 35 residues processed: 297 average time/residue: 0.8314 time to fit residues: 282.2646 Evaluate side-chains 234 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 199 time to evaluate : 1.543 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 31 residues processed: 5 average time/residue: 0.1664 time to fit residues: 3.5184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN A 768 GLN A 830 ASN A1017 ASN B 664 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.6885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 14061 Z= 0.370 Angle : 0.726 13.977 18999 Z= 0.360 Chirality : 0.048 0.298 2139 Planarity : 0.005 0.073 2349 Dihedral : 13.440 116.947 2107 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer Outliers : 6.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.20), residues: 1714 helix: 0.07 (0.17), residues: 932 sheet: -1.18 (0.43), residues: 141 loop : -3.09 (0.21), residues: 641 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 230 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 41 residues processed: 295 average time/residue: 0.8733 time to fit residues: 294.1635 Evaluate side-chains 240 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 199 time to evaluate : 1.412 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 35 residues processed: 7 average time/residue: 0.1200 time to fit residues: 3.5906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 149 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 693 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.7144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 14061 Z= 0.182 Angle : 0.657 14.801 18999 Z= 0.315 Chirality : 0.044 0.278 2139 Planarity : 0.005 0.075 2349 Dihedral : 12.715 115.115 2107 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 5.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.20), residues: 1714 helix: 0.58 (0.18), residues: 915 sheet: -0.95 (0.44), residues: 141 loop : -2.94 (0.22), residues: 658 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 211 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 45 residues processed: 266 average time/residue: 0.8550 time to fit residues: 260.4019 Evaluate side-chains 232 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 187 time to evaluate : 1.588 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 39 residues processed: 8 average time/residue: 0.1788 time to fit residues: 4.6424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 0.4980 chunk 149 optimal weight: 9.9990 chunk 32 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1073 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.7349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 14061 Z= 0.165 Angle : 0.658 14.854 18999 Z= 0.315 Chirality : 0.044 0.382 2139 Planarity : 0.005 0.075 2349 Dihedral : 12.289 113.140 2107 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer Outliers : 4.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.21), residues: 1714 helix: 0.90 (0.18), residues: 910 sheet: -0.93 (0.44), residues: 136 loop : -2.91 (0.22), residues: 668 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 199 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 42 residues processed: 249 average time/residue: 0.8015 time to fit residues: 229.8505 Evaluate side-chains 230 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 188 time to evaluate : 1.565 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 37 residues processed: 7 average time/residue: 0.3317 time to fit residues: 5.2604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 92 optimal weight: 0.0870 chunk 165 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 927 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.7700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 14061 Z= 0.312 Angle : 0.699 15.260 18999 Z= 0.341 Chirality : 0.047 0.339 2139 Planarity : 0.005 0.077 2349 Dihedral : 12.686 115.129 2107 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer Outliers : 4.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.21), residues: 1714 helix: 0.67 (0.18), residues: 922 sheet: -0.78 (0.45), residues: 136 loop : -2.93 (0.22), residues: 656 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 194 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 47 residues processed: 245 average time/residue: 0.8297 time to fit residues: 234.9471 Evaluate side-chains 234 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 187 time to evaluate : 1.571 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 40 residues processed: 8 average time/residue: 0.3373 time to fit residues: 5.7155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 81 optimal weight: 0.1980 chunk 15 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 158 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.7847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 14061 Z= 0.214 Angle : 0.668 15.742 18999 Z= 0.319 Chirality : 0.045 0.348 2139 Planarity : 0.004 0.076 2349 Dihedral : 12.240 114.602 2107 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 3.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.21), residues: 1714 helix: 0.95 (0.18), residues: 909 sheet: -0.75 (0.46), residues: 130 loop : -2.87 (0.22), residues: 675 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 185 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 38 residues processed: 231 average time/residue: 0.7839 time to fit residues: 210.0393 Evaluate side-chains 218 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 180 time to evaluate : 1.588 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 37 residues processed: 2 average time/residue: 0.1857 time to fit residues: 2.7377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 92 optimal weight: 0.0980 chunk 67 optimal weight: 0.0370 chunk 121 optimal weight: 0.9980 chunk 47 optimal weight: 0.0270 chunk 139 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 927 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.7933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 14061 Z= 0.155 Angle : 0.676 17.324 18999 Z= 0.314 Chirality : 0.044 0.323 2139 Planarity : 0.005 0.088 2349 Dihedral : 11.624 110.153 2107 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 3.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.21), residues: 1714 helix: 1.34 (0.18), residues: 897 sheet: -0.65 (0.47), residues: 131 loop : -2.76 (0.22), residues: 686 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 190 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 36 residues processed: 232 average time/residue: 0.8004 time to fit residues: 214.9348 Evaluate side-chains 214 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 178 time to evaluate : 1.609 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 32 residues processed: 5 average time/residue: 0.3840 time to fit residues: 4.6205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 108 optimal weight: 0.0060 chunk 145 optimal weight: 0.0170 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 724 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.8006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 14061 Z= 0.156 Angle : 0.671 16.907 18999 Z= 0.315 Chirality : 0.044 0.346 2139 Planarity : 0.004 0.077 2349 Dihedral : 11.335 102.795 2107 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1714 helix: 1.36 (0.18), residues: 908 sheet: -0.59 (0.47), residues: 131 loop : -2.78 (0.23), residues: 675 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 188 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 35 residues processed: 224 average time/residue: 0.8524 time to fit residues: 220.5618 Evaluate side-chains 219 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 1.463 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 32 residues processed: 4 average time/residue: 0.1818 time to fit residues: 3.3216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 7 optimal weight: 0.0050 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 927 ASN B 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.117820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.082915 restraints weight = 24630.904| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.19 r_work: 0.3082 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.8065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 14061 Z= 0.197 Angle : 0.693 16.528 18999 Z= 0.325 Chirality : 0.045 0.346 2139 Planarity : 0.004 0.077 2349 Dihedral : 11.354 102.493 2107 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.21), residues: 1714 helix: 1.37 (0.18), residues: 905 sheet: -0.71 (0.45), residues: 138 loop : -2.80 (0.23), residues: 671 =============================================================================== Job complete usr+sys time: 4890.97 seconds wall clock time: 87 minutes 36.43 seconds (5256.43 seconds total)