Starting phenix.real_space_refine (version: dev) on Mon Dec 12 10:29:52 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egg_31116/12_2022/7egg_31116.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egg_31116/12_2022/7egg_31116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egg_31116/12_2022/7egg_31116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egg_31116/12_2022/7egg_31116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egg_31116/12_2022/7egg_31116.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egg_31116/12_2022/7egg_31116.pdb" } resolution = 2.77 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= -0.000 sd= 0.100 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "D ARG 881": "NH1" <-> "NH2" Residue "D GLU 884": "OE1" <-> "OE2" Residue "D ARG 909": "NH1" <-> "NH2" Residue "D GLU 954": "OE1" <-> "OE2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "E GLU 235": "OE1" <-> "OE2" Residue "E PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 270": "OD1" <-> "OD2" Residue "E TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 347": "NH1" <-> "NH2" Residue "E ARG 450": "NH1" <-> "NH2" Residue "E ARG 452": "NH1" <-> "NH2" Residue "E GLU 563": "OE1" <-> "OE2" Residue "E PHE 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 607": "NH1" <-> "NH2" Residue "H ARG 113": "NH1" <-> "NH2" Residue "I TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 119": "NH1" <-> "NH2" Residue "J GLU 124": "OE1" <-> "OE2" Residue "L GLU 74": "OE1" <-> "OE2" Residue "L ARG 104": "NH1" <-> "NH2" Residue "L ARG 106": "NH1" <-> "NH2" Residue "L GLU 121": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 10062 Number of models: 1 Model: "" Number of chains: 7 Chain: "D" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1271 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 4376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4376 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 524} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1137 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 134} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "H" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 977 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 13, 'TRANS': 112} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 108} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 720 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 6, 'TRANS': 83} Chain breaks: 1 Chain: "L" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 622 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Time building chain proxies: 6.18, per 1000 atoms: 0.61 Number of scatterers: 10062 At special positions: 0 Unit cell: (113.16, 96.76, 104.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1903 8.00 N 1737 7.00 C 6374 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.04 Conformation dependent library (CDL) restraints added in 1.5 seconds 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2406 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 12 sheets defined 45.5% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'D' and resid 842 through 857 removed outlier: 3.739A pdb=" N SER D 846 " --> pdb=" O GLY D 842 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU D 848 " --> pdb=" O ASN D 844 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE D 852 " --> pdb=" O GLU D 848 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU D 853 " --> pdb=" O SER D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 874 through 886 removed outlier: 3.682A pdb=" N ARG D 880 " --> pdb=" O ALA D 876 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE D 885 " --> pdb=" O ARG D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 898 through 922 removed outlier: 3.638A pdb=" N SER D 903 " --> pdb=" O VAL D 899 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN D 912 " --> pdb=" O GLN D 908 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS D 916 " --> pdb=" O ASN D 912 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR D 920 " --> pdb=" O LYS D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 970 removed outlier: 3.891A pdb=" N GLN D 943 " --> pdb=" O ASP D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 1059 through 1066 removed outlier: 3.619A pdb=" N LEU D1063 " --> pdb=" O ASN D1059 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS D1066 " --> pdb=" O ASP D1062 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1083 Processing helix chain 'D' and resid 1084 through 1085 No H-bonds generated for 'chain 'D' and resid 1084 through 1085' Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 213 through 227 removed outlier: 3.841A pdb=" N SER E 219 " --> pdb=" O GLU E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 237 removed outlier: 3.811A pdb=" N ALA E 234 " --> pdb=" O ASP E 230 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU E 235 " --> pdb=" O CYS E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 254 removed outlier: 3.696A pdb=" N LEU E 243 " --> pdb=" O LEU E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 268 Processing helix chain 'E' and resid 269 through 271 No H-bonds generated for 'chain 'E' and resid 269 through 271' Processing helix chain 'E' and resid 272 through 274 No H-bonds generated for 'chain 'E' and resid 272 through 274' Processing helix chain 'E' and resid 275 through 285 Processing helix chain 'E' and resid 287 through 292 removed outlier: 3.802A pdb=" N MET E 291 " --> pdb=" O LYS E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 303 removed outlier: 3.709A pdb=" N THR E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 319 removed outlier: 4.309A pdb=" N LEU E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 327 removed outlier: 3.511A pdb=" N ASN E 326 " --> pdb=" O GLU E 323 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN E 327 " --> pdb=" O LYS E 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 323 through 327' Processing helix chain 'E' and resid 328 through 337 Processing helix chain 'E' and resid 348 through 356 removed outlier: 3.906A pdb=" N ALA E 354 " --> pdb=" O GLN E 350 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET E 355 " --> pdb=" O GLN E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 449 removed outlier: 3.536A pdb=" N LYS E 440 " --> pdb=" O ASP E 436 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE E 441 " --> pdb=" O LYS E 437 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET E 442 " --> pdb=" O LEU E 438 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS E 445 " --> pdb=" O ILE E 441 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU E 446 " --> pdb=" O MET E 442 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS E 449 " --> pdb=" O LYS E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 516 removed outlier: 3.700A pdb=" N LEU E 515 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE E 516 " --> pdb=" O ASP E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 527 Processing helix chain 'E' and resid 741 through 745 removed outlier: 4.192A pdb=" N GLU E 745 " --> pdb=" O LYS E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 764 through 768 Processing helix chain 'F' and resid 15 through 25 removed outlier: 3.750A pdb=" N MET F 19 " --> pdb=" O PRO F 15 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 61 removed outlier: 3.556A pdb=" N LEU F 39 " --> pdb=" O THR F 35 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR F 40 " --> pdb=" O CYS F 36 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER F 44 " --> pdb=" O THR F 40 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS F 56 " --> pdb=" O GLN F 52 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE F 57 " --> pdb=" O ASP F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 78 removed outlier: 4.195A pdb=" N ILE F 71 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 120 removed outlier: 3.530A pdb=" N THR F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 49 removed outlier: 3.511A pdb=" N HIS H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG H 33 " --> pdb=" O TYR H 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU H 37 " --> pdb=" O ARG H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 83 removed outlier: 3.517A pdb=" N LYS H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR H 83 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 103 through 105 No H-bonds generated for 'chain 'H' and resid 103 through 105' Processing helix chain 'H' and resid 106 through 112 removed outlier: 3.872A pdb=" N LYS H 112 " --> pdb=" O PRO H 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 26 removed outlier: 3.574A pdb=" N MET I 18 " --> pdb=" O LYS I 14 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA I 20 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN I 21 " --> pdb=" O GLN I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 62 removed outlier: 4.412A pdb=" N ILE I 36 " --> pdb=" O GLU I 32 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN I 37 " --> pdb=" O PRO I 33 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN I 38 " --> pdb=" O ARG I 34 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP I 52 " --> pdb=" O THR I 48 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP I 53 " --> pdb=" O THR I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 77 removed outlier: 3.552A pdb=" N VAL I 71 " --> pdb=" O ASP I 67 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN I 76 " --> pdb=" O ARG I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 100 removed outlier: 3.675A pdb=" N ASP I 94 " --> pdb=" O ASP I 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 123 Processing helix chain 'J' and resid 131 through 141 removed outlier: 3.689A pdb=" N TYR J 137 " --> pdb=" O ALA J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 177 Processing helix chain 'J' and resid 196 through 204 Proline residue: J 202 - end of helix Processing helix chain 'L' and resid 61 through 71 removed outlier: 3.952A pdb=" N VAL L 70 " --> pdb=" O LEU L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 106 Processing helix chain 'L' and resid 112 through 123 removed outlier: 3.715A pdb=" N VAL L 116 " --> pdb=" O GLU L 112 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS L 119 " --> pdb=" O ASP L 115 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 934 through 936 Processing sheet with id=AA2, first strand: chain 'D' and resid 1056 through 1058 removed outlier: 6.394A pdb=" N THR D1056 " --> pdb=" O GLN L 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 308 through 310 Processing sheet with id=AA4, first strand: chain 'E' and resid 782 through 785 removed outlier: 3.726A pdb=" N GLY E 795 " --> pdb=" O TYR E 464 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE E 461 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 473 through 478 removed outlier: 3.998A pdb=" N THR E 493 " --> pdb=" O PHE E 489 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 504 through 507 removed outlier: 3.719A pdb=" N SER E 506 " --> pdb=" O THR E 532 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N THR E 532 " --> pdb=" O SER E 506 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 546 through 550 removed outlier: 3.505A pdb=" N SER E 562 " --> pdb=" O THR E 566 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR E 566 " --> pdb=" O SER E 562 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL E 579 " --> pdb=" O LEU E 569 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 588 through 593 Processing sheet with id=AA9, first strand: chain 'E' and resid 634 through 635 removed outlier: 3.615A pdb=" N ARG E 663 " --> pdb=" O LEU E 653 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP E 655 " --> pdb=" O CYS E 661 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N CYS E 661 " --> pdb=" O ASP E 655 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 672 through 677 removed outlier: 6.385A pdb=" N VAL E 693 " --> pdb=" O GLU E 706 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU E 706 " --> pdb=" O VAL E 693 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU E 695 " --> pdb=" O VAL E 704 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 714 through 719 removed outlier: 4.181A pdb=" N THR E 734 " --> pdb=" O SER E 730 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL E 735 " --> pdb=" O THR E 772 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THR E 772 " --> pdb=" O VAL E 735 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU E 737 " --> pdb=" O LEU E 770 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 86 through 88 415 hydrogen bonds defined for protein. 1215 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: 3.35 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1688 1.28 - 1.41: 2540 1.41 - 1.55: 5954 1.55 - 1.68: 16 1.68 - 1.81: 78 Bond restraints: 10276 Sorted by residual: bond pdb=" C ASN H 28 " pdb=" O ASN H 28 " ideal model delta sigma weight residual 1.237 1.149 0.088 1.17e-02 7.31e+03 5.64e+01 bond pdb=" C ASP H 27 " pdb=" O ASP H 27 " ideal model delta sigma weight residual 1.237 1.151 0.085 1.19e-02 7.06e+03 5.14e+01 bond pdb=" C LEU H 31 " pdb=" O LEU H 31 " ideal model delta sigma weight residual 1.237 1.162 0.075 1.19e-02 7.06e+03 3.96e+01 bond pdb=" C LEU E 524 " pdb=" O LEU E 524 " ideal model delta sigma weight residual 1.237 1.303 -0.066 1.17e-02 7.31e+03 3.22e+01 bond pdb=" C TYR J 193 " pdb=" O TYR J 193 " ideal model delta sigma weight residual 1.242 1.196 0.046 1.00e-02 1.00e+04 2.08e+01 ... (remaining 10271 not shown) Histogram of bond angle deviations from ideal: 99.37 - 107.18: 450 107.18 - 114.98: 5979 114.98 - 122.78: 6362 122.78 - 130.58: 1067 130.58 - 138.39: 56 Bond angle restraints: 13914 Sorted by residual: angle pdb=" N THR E 756 " pdb=" CA THR E 756 " pdb=" C THR E 756 " ideal model delta sigma weight residual 113.50 103.21 10.29 1.23e+00 6.61e-01 7.01e+01 angle pdb=" N ALA H 32 " pdb=" CA ALA H 32 " pdb=" C ALA H 32 " ideal model delta sigma weight residual 111.07 102.26 8.81 1.07e+00 8.73e-01 6.78e+01 angle pdb=" N ASP H 27 " pdb=" CA ASP H 27 " pdb=" C ASP H 27 " ideal model delta sigma weight residual 111.36 102.78 8.58 1.09e+00 8.42e-01 6.19e+01 angle pdb=" N PRO E 762 " pdb=" CA PRO E 762 " pdb=" C PRO E 762 " ideal model delta sigma weight residual 114.27 124.27 -10.00 1.35e+00 5.49e-01 5.49e+01 angle pdb=" C ASP J 148 " pdb=" N PRO J 149 " pdb=" CA PRO J 149 " ideal model delta sigma weight residual 119.05 125.82 -6.77 1.11e+00 8.12e-01 3.72e+01 ... (remaining 13909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 5555 17.58 - 35.17: 565 35.17 - 52.75: 121 52.75 - 70.33: 10 70.33 - 87.92: 7 Dihedral angle restraints: 6258 sinusoidal: 2557 harmonic: 3701 Sorted by residual: dihedral pdb=" C GLU H 51 " pdb=" N GLU H 51 " pdb=" CA GLU H 51 " pdb=" CB GLU H 51 " ideal model delta harmonic sigma weight residual -122.60 -106.45 -16.15 0 2.50e+00 1.60e-01 4.17e+01 dihedral pdb=" CA PRO H 156 " pdb=" C PRO H 156 " pdb=" N HIS H 157 " pdb=" CA HIS H 157 " ideal model delta harmonic sigma weight residual 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA TYR E 470 " pdb=" C TYR E 470 " pdb=" N GLN E 471 " pdb=" CA GLN E 471 " ideal model delta harmonic sigma weight residual 180.00 152.27 27.73 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 6255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1380 0.118 - 0.236: 129 0.236 - 0.354: 35 0.354 - 0.472: 5 0.472 - 0.590: 2 Chirality restraints: 1551 Sorted by residual: chirality pdb=" CA PRO H 25 " pdb=" N PRO H 25 " pdb=" C PRO H 25 " pdb=" CB PRO H 25 " both_signs ideal model delta sigma weight residual False 2.72 2.13 0.59 2.00e-01 2.50e+01 8.69e+00 chirality pdb=" CA ASN H 28 " pdb=" N ASN H 28 " pdb=" C ASN H 28 " pdb=" CB ASN H 28 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.30e+00 chirality pdb=" CA GLU H 51 " pdb=" N GLU H 51 " pdb=" C GLU H 51 " pdb=" CB GLU H 51 " both_signs ideal model delta sigma weight residual False 2.51 2.97 -0.46 2.00e-01 2.50e+01 5.33e+00 ... (remaining 1548 not shown) Planarity restraints: 1802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 769 " 0.022 2.00e-02 2.50e+03 4.54e-02 2.06e+01 pdb=" C LEU E 769 " -0.079 2.00e-02 2.50e+03 pdb=" O LEU E 769 " 0.030 2.00e-02 2.50e+03 pdb=" N LEU E 770 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE L 92 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C ILE L 92 " 0.057 2.00e-02 2.50e+03 pdb=" O ILE L 92 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU L 93 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER J 147 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C SER J 147 " 0.056 2.00e-02 2.50e+03 pdb=" O SER J 147 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP J 148 " -0.019 2.00e-02 2.50e+03 ... (remaining 1799 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2183 2.78 - 3.31: 9049 3.31 - 3.84: 16913 3.84 - 4.37: 21839 4.37 - 4.90: 35515 Nonbonded interactions: 85499 Sorted by model distance: nonbonded pdb=" N ASP L 79 " pdb=" OD1 ASP L 79 " model vdw 2.248 2.520 nonbonded pdb=" OG SER E 562 " pdb=" OD1 ASP E 564 " model vdw 2.277 2.440 nonbonded pdb=" OH TYR D1080 " pdb=" OD2 ASP E 606 " model vdw 2.300 2.440 nonbonded pdb=" OG1 THR E 479 " pdb=" O ASP E 481 " model vdw 2.306 2.440 nonbonded pdb=" OD1 ASP E 732 " pdb=" OG1 THR E 734 " model vdw 2.313 2.440 ... (remaining 85494 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6374 2.51 5 N 1737 2.21 5 O 1903 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 8.260 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.090 Process input model: 30.090 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:13.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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 : 0.008 0.088 10276 Z= 0.488 Angle : 1.131 13.388 13914 Z= 0.764 Chirality : 0.082 0.590 1551 Planarity : 0.008 0.076 1802 Dihedral : 14.566 87.919 3852 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Rotamer Outliers : 3.51 % Cbeta Deviations : 1.16 % 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: -3.25 (0.21), residues: 1233 helix: -2.37 (0.19), residues: 567 sheet: -1.37 (0.41), residues: 140 loop : -1.94 (0.24), residues: 526 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 272 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 13 residues processed: 300 average time/residue: 1.2057 time to fit residues: 388.6571 Evaluate side-chains 223 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 210 time to evaluate : 1.212 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 3 average time/residue: 0.8014 time to fit residues: 4.3462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 856 ASN D 936 GLN E 223 HIS E 232 HIS E 254 ASN E 256 HIS E 258 ASN E 268 HIS E 326 ASN E 350 GLN E 351 GLN E 616 HIS E 636 HIS E 640 ASN E 673 HIS F 52 GLN F 89 GLN F 119 ASN H 145 HIS I 21 GLN I 38 GLN I 98 GLN ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 210 ASN L 73 ASN L 117 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 10276 Z= 0.209 Angle : 0.586 10.279 13914 Z= 0.305 Chirality : 0.042 0.145 1551 Planarity : 0.005 0.061 1802 Dihedral : 5.132 24.824 1365 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Rotamer Outliers : 5.32 % 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: -1.81 (0.22), residues: 1233 helix: -0.96 (0.21), residues: 568 sheet: -0.55 (0.44), residues: 133 loop : -1.50 (0.24), residues: 532 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 229 time to evaluate : 1.239 Fit side-chains outliers start: 59 outliers final: 23 residues processed: 260 average time/residue: 1.2183 time to fit residues: 341.2533 Evaluate side-chains 228 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 205 time to evaluate : 1.266 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 16 residues processed: 7 average time/residue: 0.5857 time to fit residues: 6.5792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 0.0970 chunk 92 optimal weight: 0.4980 chunk 76 optimal weight: 0.0970 chunk 30 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 856 ASN E 315 GLN ** I 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 160 GLN J 210 ASN L 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 10276 Z= 0.152 Angle : 0.525 10.160 13914 Z= 0.267 Chirality : 0.040 0.141 1551 Planarity : 0.005 0.054 1802 Dihedral : 4.596 22.524 1365 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.41 % Favored : 96.51 % Rotamer Outliers : 4.41 % 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: -0.85 (0.23), residues: 1233 helix: 0.06 (0.22), residues: 566 sheet: -0.46 (0.43), residues: 133 loop : -1.19 (0.25), residues: 534 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 205 time to evaluate : 1.256 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 20 residues processed: 232 average time/residue: 1.1874 time to fit residues: 297.6096 Evaluate side-chains 215 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 195 time to evaluate : 1.339 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.1086 time to fit residues: 2.4808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 315 GLN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 210 ASN ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 10276 Z= 0.270 Angle : 0.568 9.595 13914 Z= 0.290 Chirality : 0.042 0.151 1551 Planarity : 0.005 0.054 1802 Dihedral : 4.718 23.558 1365 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.54 % Rotamer Outliers : 4.77 % 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: -0.56 (0.24), residues: 1233 helix: 0.32 (0.22), residues: 568 sheet: -0.36 (0.43), residues: 134 loop : -1.06 (0.26), residues: 531 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 199 time to evaluate : 1.503 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 26 residues processed: 229 average time/residue: 1.1670 time to fit residues: 290.0321 Evaluate side-chains 220 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 194 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 18 residues processed: 8 average time/residue: 0.2954 time to fit residues: 4.6678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 82 optimal weight: 0.0270 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 30 optimal weight: 0.0970 chunk 40 optimal weight: 0.9980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 911 GLN E 315 GLN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 10276 Z= 0.145 Angle : 0.515 9.887 13914 Z= 0.258 Chirality : 0.040 0.140 1551 Planarity : 0.004 0.051 1802 Dihedral : 4.332 21.729 1365 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.33 % Favored : 96.59 % Rotamer Outliers : 4.14 % 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: -0.13 (0.24), residues: 1233 helix: 0.78 (0.23), residues: 567 sheet: -0.34 (0.43), residues: 136 loop : -0.89 (0.26), residues: 530 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 197 time to evaluate : 1.258 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 25 residues processed: 222 average time/residue: 1.1302 time to fit residues: 271.2827 Evaluate side-chains 216 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 191 time to evaluate : 1.073 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 19 residues processed: 7 average time/residue: 0.4186 time to fit residues: 5.2063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 315 GLN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 10276 Z= 0.293 Angle : 0.566 9.209 13914 Z= 0.287 Chirality : 0.043 0.152 1551 Planarity : 0.004 0.051 1802 Dihedral : 4.590 23.344 1365 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.54 % Favored : 95.38 % Rotamer Outliers : 4.05 % 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: -0.11 (0.24), residues: 1233 helix: 0.74 (0.23), residues: 570 sheet: -0.34 (0.42), residues: 137 loop : -0.83 (0.27), residues: 526 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 194 time to evaluate : 1.216 Fit side-chains outliers start: 45 outliers final: 26 residues processed: 220 average time/residue: 1.1083 time to fit residues: 263.6064 Evaluate side-chains 215 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 19 residues processed: 8 average time/residue: 0.5003 time to fit residues: 6.1744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 315 GLN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 ASN L 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10276 Z= 0.182 Angle : 0.530 9.568 13914 Z= 0.265 Chirality : 0.040 0.143 1551 Planarity : 0.004 0.050 1802 Dihedral : 4.382 22.575 1365 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Rotamer Outliers : 3.51 % 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: 0.09 (0.24), residues: 1233 helix: 0.97 (0.23), residues: 568 sheet: -0.31 (0.42), residues: 136 loop : -0.78 (0.27), residues: 529 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 190 time to evaluate : 1.238 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 28 residues processed: 214 average time/residue: 1.2379 time to fit residues: 285.8803 Evaluate side-chains 214 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 186 time to evaluate : 1.235 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 21 residues processed: 10 average time/residue: 0.4150 time to fit residues: 6.7482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 0.0010 chunk 58 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 315 GLN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 ASN L 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 10276 Z= 0.156 Angle : 0.524 9.966 13914 Z= 0.259 Chirality : 0.040 0.142 1551 Planarity : 0.004 0.049 1802 Dihedral : 4.177 21.866 1365 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.14 % Favored : 95.78 % Rotamer Outliers : 3.24 % 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: 0.29 (0.24), residues: 1233 helix: 1.17 (0.23), residues: 570 sheet: -0.25 (0.42), residues: 136 loop : -0.71 (0.27), residues: 527 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 196 time to evaluate : 1.236 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 20 residues processed: 221 average time/residue: 1.1398 time to fit residues: 272.3972 Evaluate side-chains 205 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 185 time to evaluate : 1.118 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 5 average time/residue: 0.4577 time to fit residues: 4.2685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 0.0070 chunk 72 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 overall best weight: 1.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 315 GLN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 10276 Z= 0.273 Angle : 0.579 9.754 13914 Z= 0.291 Chirality : 0.043 0.158 1551 Planarity : 0.004 0.049 1802 Dihedral : 4.466 23.221 1365 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.62 % Favored : 95.30 % Rotamer Outliers : 2.61 % 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: 0.24 (0.24), residues: 1233 helix: 1.08 (0.23), residues: 569 sheet: -0.29 (0.42), residues: 137 loop : -0.66 (0.27), residues: 527 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 194 time to evaluate : 1.282 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 20 residues processed: 213 average time/residue: 1.1044 time to fit residues: 254.7831 Evaluate side-chains 206 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 1.287 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 4 average time/residue: 0.7411 time to fit residues: 5.0322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 315 GLN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10276 Z= 0.183 Angle : 0.549 10.014 13914 Z= 0.273 Chirality : 0.041 0.161 1551 Planarity : 0.004 0.049 1802 Dihedral : 4.262 22.330 1365 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.22 % Favored : 95.70 % Rotamer Outliers : 2.25 % 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: 0.37 (0.24), residues: 1233 helix: 1.22 (0.23), residues: 570 sheet: -0.24 (0.42), residues: 136 loop : -0.64 (0.27), residues: 527 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 189 time to evaluate : 1.229 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 21 residues processed: 208 average time/residue: 1.1398 time to fit residues: 256.5197 Evaluate side-chains 206 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 185 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 4 average time/residue: 1.0387 time to fit residues: 6.0479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 0.0040 chunk 27 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 100 optimal weight: 0.0470 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 overall best weight: 0.5090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 315 GLN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 ASN I 60 HIS L 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.144573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118685 restraints weight = 12528.279| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.00 r_work: 0.3363 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 10276 Z= 0.157 Angle : 0.532 10.356 13914 Z= 0.264 Chirality : 0.040 0.156 1551 Planarity : 0.004 0.049 1802 Dihedral : 4.082 21.485 1365 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.14 % Favored : 95.78 % Rotamer Outliers : 2.07 % 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 (0.24), residues: 1233 helix: 1.34 (0.23), residues: 570 sheet: -0.22 (0.42), residues: 136 loop : -0.61 (0.27), residues: 527 =============================================================================== Job complete usr+sys time: 4628.93 seconds wall clock time: 82 minutes 28.16 seconds (4948.16 seconds total)