Starting phenix.real_space_refine on Sat Mar 16 05:19:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npl_0473/03_2024/6npl_0473_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npl_0473/03_2024/6npl_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_0473/03_2024/6npl_0473.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npl_0473/03_2024/6npl_0473.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npl_0473/03_2024/6npl_0473_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npl_0473/03_2024/6npl_0473_updated.pdb" } resolution = 2.9 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= 0.003 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 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. 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.27, per 1000 atoms: 0.53 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: 5.18 Conformation dependent library (CDL) restraints added in 2.4 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: 3.14 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: 4.08 Time building geometry restraints manager: 5.61 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: 7830 27.83 - 55.67: 443 55.67 - 83.50: 60 83.50 - 111.34: 8 111.34 - 139.17: 6 Dihedral angle restraints: 8347 sinusoidal: 3399 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 8344 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 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: 0.530 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: 3.100 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 37.590 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 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 : 17.241 139.172 5169 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 % Allowed : 12.55 % Favored : 79.78 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 639 HIS 0.007 0.001 HIS A 512 PHE 0.033 0.003 PHE B 606 TYR 0.025 0.002 TYR A 676 ARG 0.006 0.001 ARG B 404 *********************** 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 : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 829 ILE cc_start: 0.6776 (mm) cc_final: 0.6489 (mm) REVERT: A 852 ASP cc_start: -0.0087 (OUTLIER) cc_final: -0.0400 (m-30) REVERT: B 384 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7630 (pttm) REVERT: B 1057 ARG cc_start: 0.4119 (OUTLIER) cc_final: 0.3007 (mmt180) outliers start: 110 outliers final: 19 residues processed: 437 average time/residue: 0.8975 time to fit residues: 441.7246 Evaluate side-chains 236 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 214 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 1057 ARG Chi-restraints excluded: chain B residue 1124 VAL 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: 0.9990 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: 0.8980 chunk 100 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14061 Z= 0.238 Angle : 0.837 33.381 18999 Z= 0.377 Chirality : 0.044 0.224 2139 Planarity : 0.005 0.071 2349 Dihedral : 14.703 118.527 2188 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 6.49 % Allowed : 20.99 % Favored : 72.52 % 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: -2.71 (0.19), residues: 1714 helix: -0.76 (0.16), residues: 916 sheet: -1.61 (0.42), residues: 140 loop : -3.34 (0.20), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 209 HIS 0.004 0.001 HIS B 991 PHE 0.026 0.002 PHE B 369 TYR 0.017 0.002 TYR B 965 ARG 0.008 0.001 ARG B 803 *********************** 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 356 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 263 time to evaluate : 1.618 Fit side-chains revert: symmetry clash REVERT: A 384 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6315 (pttm) REVERT: A 508 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7263 (ttmm) REVERT: A 852 ASP cc_start: 0.0744 (OUTLIER) cc_final: 0.0154 (m-30) REVERT: B 304 MET cc_start: 0.8421 (ttp) cc_final: 0.8207 (ttt) REVERT: B 483 THR cc_start: 0.7602 (p) cc_final: 0.7375 (m) REVERT: B 719 MET cc_start: 0.6477 (mmm) cc_final: 0.5524 (tmt) REVERT: B 987 ASN cc_start: 0.6277 (OUTLIER) cc_final: 0.5839 (t0) REVERT: B 1031 MET cc_start: 0.5734 (ttp) cc_final: 0.5450 (ttt) outliers start: 93 outliers final: 27 residues processed: 324 average time/residue: 0.8420 time to fit residues: 310.3221 Evaluate side-chains 239 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 208 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1009 ASP Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 821 ASP Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 975 ASP Chi-restraints excluded: chain B residue 987 ASN Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1050 LEU 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: 3.9990 chunk 129 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 169 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 B1073 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14061 Z= 0.254 Angle : 0.826 31.844 18999 Z= 0.368 Chirality : 0.046 0.466 2139 Planarity : 0.005 0.074 2349 Dihedral : 13.944 111.302 2155 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 5.72 % Allowed : 23.43 % Favored : 70.85 % 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: -2.02 (0.19), residues: 1714 helix: -0.09 (0.17), residues: 916 sheet: -1.40 (0.42), residues: 143 loop : -3.18 (0.21), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 209 HIS 0.005 0.001 HIS A 512 PHE 0.021 0.002 PHE A 954 TYR 0.014 0.002 TYR B 276 ARG 0.015 0.001 ARG A1098 *********************** 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 324 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 242 time to evaluate : 1.625 Fit side-chains revert: symmetry clash REVERT: A 478 LEU cc_start: 0.6492 (OUTLIER) cc_final: 0.6163 (mt) REVERT: A 719 MET cc_start: 0.6133 (mmm) cc_final: 0.5153 (tmt) REVERT: A 811 ILE cc_start: 0.8300 (pt) cc_final: 0.7962 (pt) REVERT: A 852 ASP cc_start: 0.1212 (OUTLIER) cc_final: 0.0508 (m-30) REVERT: B 324 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6988 (ptp) REVERT: B 325 ILE cc_start: 0.6827 (OUTLIER) cc_final: 0.6565 (mt) REVERT: B 483 THR cc_start: 0.7603 (p) cc_final: 0.7340 (m) REVERT: B 719 MET cc_start: 0.6736 (mmm) cc_final: 0.6110 (tmt) REVERT: B 932 ARG cc_start: 0.5127 (OUTLIER) cc_final: 0.4763 (ppt170) outliers start: 82 outliers final: 24 residues processed: 300 average time/residue: 0.8798 time to fit residues: 300.0208 Evaluate side-chains 225 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 196 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 932 ARG Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 975 ASP Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1131 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 5.9990 chunk 117 optimal weight: 0.1980 chunk 81 optimal weight: 10.0000 chunk 17 optimal weight: 0.0050 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 148 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 overall best weight: 1.2398 ------------------------------------------------------------------------------- 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 830 ASN B 664 ASN B 830 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.6163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14061 Z= 0.209 Angle : 0.807 32.956 18999 Z= 0.353 Chirality : 0.044 0.329 2139 Planarity : 0.005 0.077 2349 Dihedral : 13.399 110.773 2153 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 4.88 % Allowed : 25.24 % Favored : 69.87 % 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: -1.48 (0.20), residues: 1714 helix: 0.43 (0.18), residues: 909 sheet: -0.98 (0.44), residues: 138 loop : -3.07 (0.21), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 770 HIS 0.010 0.001 HIS A1128 PHE 0.022 0.002 PHE B 813 TYR 0.010 0.001 TYR B 828 ARG 0.007 0.001 ARG A 713 *********************** 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 287 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 217 time to evaluate : 1.568 Fit side-chains revert: symmetry clash REVERT: A 478 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6258 (mt) REVERT: A 719 MET cc_start: 0.6325 (mmm) cc_final: 0.5370 (tmt) REVERT: A 811 ILE cc_start: 0.8324 (pt) cc_final: 0.7979 (pt) REVERT: A 852 ASP cc_start: 0.1103 (OUTLIER) cc_final: 0.0287 (m-30) REVERT: A 1031 MET cc_start: 0.6559 (ppp) cc_final: 0.6271 (ppp) REVERT: B 225 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.5998 (mpt) REVERT: B 325 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6613 (mt) REVERT: B 395 LEU cc_start: 0.8683 (tm) cc_final: 0.8426 (tp) REVERT: B 483 THR cc_start: 0.7617 (p) cc_final: 0.7334 (m) REVERT: B 719 MET cc_start: 0.7078 (mmm) cc_final: 0.5967 (tmt) REVERT: B 823 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7818 (pmtt) REVERT: B 932 ARG cc_start: 0.5233 (OUTLIER) cc_final: 0.5029 (ppt170) outliers start: 70 outliers final: 25 residues processed: 261 average time/residue: 0.7551 time to fit residues: 228.6055 Evaluate side-chains 227 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 196 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 823 LYS Chi-restraints excluded: chain B residue 840 TYR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 932 ARG Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 975 ASP Chi-restraints excluded: chain B residue 1040 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 A 768 GLN A 833 HIS A1017 ASN B 830 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.7357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 14061 Z= 0.393 Angle : 0.880 32.510 18999 Z= 0.398 Chirality : 0.049 0.371 2139 Planarity : 0.005 0.075 2349 Dihedral : 13.902 115.752 2153 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 5.65 % Allowed : 25.24 % Favored : 69.11 % 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: -1.54 (0.20), residues: 1714 helix: 0.30 (0.17), residues: 923 sheet: -0.94 (0.44), residues: 137 loop : -3.05 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 952 HIS 0.007 0.001 HIS B 512 PHE 0.028 0.002 PHE A 606 TYR 0.020 0.002 TYR B 828 ARG 0.016 0.001 ARG B1038 *********************** 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: 81 poor density : 202 time to evaluate : 1.556 Fit side-chains revert: symmetry clash REVERT: A 330 ASP cc_start: 0.7332 (p0) cc_final: 0.7065 (p0) REVERT: A 719 MET cc_start: 0.7143 (mmm) cc_final: 0.6268 (tmt) REVERT: A 811 ILE cc_start: 0.8521 (pt) cc_final: 0.8196 (pt) REVERT: A 846 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6675 (ttm-80) REVERT: A 852 ASP cc_start: 0.1568 (OUTLIER) cc_final: 0.0823 (m-30) REVERT: B 395 LEU cc_start: 0.8824 (tm) cc_final: 0.8594 (tp) REVERT: B 719 MET cc_start: 0.7302 (mmm) cc_final: 0.6011 (tmt) outliers start: 81 outliers final: 36 residues processed: 260 average time/residue: 0.8215 time to fit residues: 243.8161 Evaluate side-chains 220 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 182 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 846 ARG Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 840 TYR Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 975 ASP Chi-restraints excluded: chain B residue 978 ILE Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain B residue 1040 ASP Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1131 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 160 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN A1088 ASN B 830 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.7556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14061 Z= 0.187 Angle : 0.807 37.305 18999 Z= 0.353 Chirality : 0.045 0.362 2139 Planarity : 0.004 0.078 2349 Dihedral : 13.107 114.832 2153 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.46 % Allowed : 26.78 % Favored : 68.76 % 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: -1.09 (0.21), residues: 1714 helix: 0.80 (0.18), residues: 905 sheet: -0.96 (0.44), residues: 137 loop : -2.92 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 683 HIS 0.003 0.001 HIS A 512 PHE 0.020 0.001 PHE B 736 TYR 0.009 0.001 TYR B 828 ARG 0.007 0.001 ARG B 988 *********************** 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 257 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 193 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: A 719 MET cc_start: 0.7125 (mmm) cc_final: 0.6304 (tmt) REVERT: A 811 ILE cc_start: 0.8351 (pt) cc_final: 0.8006 (pt) REVERT: A 852 ASP cc_start: 0.1773 (OUTLIER) cc_final: 0.1008 (m-30) REVERT: B 319 ASP cc_start: 0.6527 (OUTLIER) cc_final: 0.6294 (m-30) REVERT: B 395 LEU cc_start: 0.8823 (tm) cc_final: 0.8600 (tp) REVERT: B 719 MET cc_start: 0.7134 (mmm) cc_final: 0.5828 (tmt) outliers start: 64 outliers final: 33 residues processed: 238 average time/residue: 0.7744 time to fit residues: 211.8630 Evaluate side-chains 218 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 183 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 829 ILE Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 967 ILE Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1131 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 121 optimal weight: 0.0030 chunk 140 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 165 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 76 optimal weight: 0.0870 chunk 102 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 overall best weight: 1.1772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 927 ASN B 830 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.7694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14061 Z= 0.195 Angle : 0.664 17.205 18999 Z= 0.313 Chirality : 0.045 0.348 2139 Planarity : 0.004 0.076 2349 Dihedral : 12.820 112.611 2152 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 4.18 % Allowed : 26.92 % Favored : 68.90 % 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: -0.90 (0.21), residues: 1714 helix: 0.97 (0.18), residues: 910 sheet: -0.93 (0.44), residues: 138 loop : -2.87 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 952 HIS 0.003 0.001 HIS A 620 PHE 0.019 0.001 PHE A 954 TYR 0.009 0.001 TYR B 692 ARG 0.009 0.001 ARG B 988 *********************** 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 247 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 187 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 ASP cc_start: 0.7018 (p0) cc_final: 0.6781 (p0) REVERT: A 719 MET cc_start: 0.7116 (mmm) cc_final: 0.6336 (tmt) REVERT: A 811 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8020 (pt) REVERT: A 852 ASP cc_start: 0.1785 (OUTLIER) cc_final: 0.1035 (m-30) REVERT: B 395 LEU cc_start: 0.8823 (tm) cc_final: 0.8600 (tp) REVERT: B 719 MET cc_start: 0.7137 (mmm) cc_final: 0.5842 (tmt) outliers start: 60 outliers final: 36 residues processed: 228 average time/residue: 0.8225 time to fit residues: 215.0244 Evaluate side-chains 218 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 180 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 967 ILE Chi-restraints excluded: chain B residue 975 ASP Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain B residue 1081 LYS Chi-restraints excluded: chain B residue 1131 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 0.0470 chunk 105 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 158 optimal weight: 0.7980 chunk 144 optimal weight: 7.9990 overall best weight: 1.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 830 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.7832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14061 Z= 0.194 Angle : 0.662 15.652 18999 Z= 0.314 Chirality : 0.045 0.321 2139 Planarity : 0.004 0.073 2349 Dihedral : 12.575 110.908 2152 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.91 % Allowed : 27.89 % Favored : 68.20 % 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: -0.76 (0.21), residues: 1714 helix: 1.13 (0.18), residues: 903 sheet: -0.93 (0.44), residues: 139 loop : -2.83 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 770 HIS 0.003 0.001 HIS A 620 PHE 0.025 0.001 PHE B 712 TYR 0.008 0.001 TYR A 371 ARG 0.013 0.001 ARG A 932 *********************** 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 249 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 193 time to evaluate : 1.361 Fit side-chains revert: symmetry clash REVERT: A 330 ASP cc_start: 0.7009 (p0) cc_final: 0.6777 (p0) REVERT: A 719 MET cc_start: 0.7043 (mmm) cc_final: 0.6170 (tmt) REVERT: A 811 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8049 (pt) REVERT: A 852 ASP cc_start: 0.2228 (OUTLIER) cc_final: 0.1292 (m-30) REVERT: B 395 LEU cc_start: 0.8837 (tm) cc_final: 0.8612 (tp) REVERT: B 719 MET cc_start: 0.7159 (mmm) cc_final: 0.5861 (tmt) outliers start: 56 outliers final: 32 residues processed: 231 average time/residue: 0.7713 time to fit residues: 205.1106 Evaluate side-chains 217 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 183 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 975 ASP Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain B residue 1131 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.3980 chunk 158 optimal weight: 0.9990 chunk 92 optimal weight: 0.0370 chunk 67 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 overall best weight: 0.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 693 HIS A 927 ASN B 724 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.7935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14061 Z= 0.171 Angle : 0.659 16.298 18999 Z= 0.311 Chirality : 0.044 0.339 2139 Planarity : 0.004 0.073 2349 Dihedral : 12.270 108.753 2152 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.86 % Allowed : 28.94 % Favored : 68.20 % 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: -0.60 (0.21), residues: 1714 helix: 1.34 (0.18), residues: 894 sheet: -0.89 (0.44), residues: 138 loop : -2.80 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 770 HIS 0.005 0.001 HIS A 693 PHE 0.017 0.001 PHE B 981 TYR 0.025 0.001 TYR B 965 ARG 0.015 0.001 ARG B 988 *********************** 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 229 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 188 time to evaluate : 1.516 Fit side-chains revert: symmetry clash REVERT: A 330 ASP cc_start: 0.6994 (p0) cc_final: 0.6761 (p0) REVERT: A 719 MET cc_start: 0.7075 (mmm) cc_final: 0.6225 (tmt) REVERT: A 811 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8033 (pt) REVERT: A 852 ASP cc_start: 0.1893 (OUTLIER) cc_final: 0.1532 (m-30) REVERT: B 395 LEU cc_start: 0.8828 (tm) cc_final: 0.8615 (tp) REVERT: B 719 MET cc_start: 0.7134 (mmm) cc_final: 0.5832 (tmt) outliers start: 41 outliers final: 27 residues processed: 218 average time/residue: 0.8308 time to fit residues: 207.3108 Evaluate side-chains 209 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 180 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain B residue 1131 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 105 optimal weight: 0.2980 chunk 83 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 145 optimal weight: 0.0970 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7831 moved from start: 0.8032 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= 0.175 Angle : 0.679 16.018 18999 Z= 0.317 Chirality : 0.044 0.335 2139 Planarity : 0.004 0.073 2349 Dihedral : 12.038 107.406 2152 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.37 % Allowed : 29.71 % Favored : 67.92 % 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: -0.59 (0.21), residues: 1714 helix: 1.34 (0.18), residues: 902 sheet: -0.89 (0.44), residues: 138 loop : -2.84 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 770 HIS 0.003 0.001 HIS B1128 PHE 0.028 0.001 PHE B 712 TYR 0.018 0.001 TYR B 692 ARG 0.009 0.001 ARG B 988 ********************** 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 219 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 185 time to evaluate : 1.573 Fit side-chains revert: symmetry clash REVERT: A 330 ASP cc_start: 0.6996 (p0) cc_final: 0.6774 (p0) REVERT: A 719 MET cc_start: 0.6916 (mmm) cc_final: 0.6223 (tmt) REVERT: A 811 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8065 (pt) REVERT: A 852 ASP cc_start: 0.2082 (OUTLIER) cc_final: 0.1527 (m-30) REVERT: B 395 LEU cc_start: 0.8815 (tm) cc_final: 0.8608 (tp) REVERT: B 719 MET cc_start: 0.7168 (mmm) cc_final: 0.5846 (tmt) outliers start: 34 outliers final: 24 residues processed: 207 average time/residue: 0.8412 time to fit residues: 200.1298 Evaluate side-chains 205 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 179 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1131 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 0.9980 chunk 125 optimal weight: 0.0870 chunk 20 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 17 optimal weight: 0.0980 chunk 25 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN B 220 ASN B 724 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.118446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.083112 restraints weight = 24626.004| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.13 r_work: 0.3099 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.8118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14061 Z= 0.156 Angle : 0.670 16.599 18999 Z= 0.311 Chirality : 0.044 0.341 2139 Planarity : 0.004 0.072 2349 Dihedral : 11.774 105.447 2152 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.37 % Allowed : 30.20 % Favored : 67.43 % 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: -0.44 (0.21), residues: 1714 helix: 1.48 (0.18), residues: 900 sheet: -0.80 (0.44), residues: 138 loop : -2.78 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 770 HIS 0.006 0.001 HIS A 693 PHE 0.023 0.001 PHE B 954 TYR 0.024 0.001 TYR B 965 ARG 0.015 0.000 ARG B 988 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4753.00 seconds wall clock time: 86 minutes 12.70 seconds (5172.70 seconds total)