Starting phenix.real_space_refine on Fri Mar 15 18:25:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s2e_10088/03_2024/6s2e_10088_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s2e_10088/03_2024/6s2e_10088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s2e_10088/03_2024/6s2e_10088.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s2e_10088/03_2024/6s2e_10088.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s2e_10088/03_2024/6s2e_10088_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s2e_10088/03_2024/6s2e_10088_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 68 5.16 5 C 7984 2.51 5 N 2079 2.21 5 O 2324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 53": "OE1" <-> "OE2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "A ASP 657": "OD1" <-> "OD2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A ARG 686": "NH1" <-> "NH2" Residue "A GLU 754": "OE1" <-> "OE2" Residue "A ASP 772": "OD1" <-> "OD2" Residue "A ASP 875": "OD1" <-> "OD2" Residue "A PHE 943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 945": "OE1" <-> "OE2" Residue "A GLU 991": "OE1" <-> "OE2" Residue "A ASP 1010": "OD1" <-> "OD2" Residue "A ASP 1075": "OD1" <-> "OD2" Residue "A TYR 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 51": "NH1" <-> "NH2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B GLU 279": "OE1" <-> "OE2" 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: 12459 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 8154 Classifications: {'peptide': 1006} Link IDs: {'PCIS': 2, 'PTRANS': 46, 'TRANS': 957} Chain breaks: 6 Chain: "D" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1031 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 125} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 225 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "B" Number of atoms: 3041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3041 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4761 SG CYS A 677 74.994 35.130 17.630 1.00143.72 S ATOM 4690 SG CYS A 668 72.088 29.439 18.791 1.00135.31 S ATOM 4963 SG CYS A 763 75.014 33.159 23.280 1.00114.07 S ATOM 4673 SG CYS A 665 77.473 29.916 18.710 1.00136.78 S Time building chain proxies: 6.99, per 1000 atoms: 0.56 Number of scatterers: 12459 At special positions: 0 Unit cell: (126.557, 128.684, 103.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 68 16.00 O 2324 8.00 N 2079 7.00 C 7984 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: 5.17 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1401 " pdb="FE1 SF4 A1401 " - pdb=" SG CYS A 677 " pdb="FE4 SF4 A1401 " - pdb=" SG CYS A 665 " pdb="FE3 SF4 A1401 " - pdb=" SG CYS A 763 " pdb="FE2 SF4 A1401 " - pdb=" SG CYS A 668 " Number of angles added : 12 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2924 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 18 sheets defined 36.4% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 33 through 49 Processing helix chain 'A' and resid 146 through 159 removed outlier: 5.015A pdb=" N ASN A 150 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A 153 " --> pdb=" O ASN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 196 through 211 Proline residue: A 208 - end of helix Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 355 through 369 Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 422 through 429 Processing helix chain 'A' and resid 434 through 436 No H-bonds generated for 'chain 'A' and resid 434 through 436' Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 456 through 465 Proline residue: A 461 - end of helix removed outlier: 4.051A pdb=" N PHE A 464 " --> pdb=" O THR A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 498 removed outlier: 4.825A pdb=" N HIS A 490 " --> pdb=" O MET A 486 " (cutoff:3.500A) Proline residue: A 491 - end of helix Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 512 through 526 Processing helix chain 'A' and resid 578 through 597 Proline residue: A 589 - end of helix Processing helix chain 'A' and resid 604 through 606 No H-bonds generated for 'chain 'A' and resid 604 through 606' Processing helix chain 'A' and resid 610 through 626 Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 656 through 658 No H-bonds generated for 'chain 'A' and resid 656 through 658' Processing helix chain 'A' and resid 770 through 797 Processing helix chain 'A' and resid 807 through 835 removed outlier: 3.710A pdb=" N PHE A 830 " --> pdb=" O ILE A 826 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TYR A 831 " --> pdb=" O LEU A 827 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY A 832 " --> pdb=" O ASN A 828 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL A 834 " --> pdb=" O PHE A 830 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N MET A 835 " --> pdb=" O TYR A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 868 Processing helix chain 'A' and resid 905 through 918 Processing helix chain 'A' and resid 993 through 1007 removed outlier: 4.731A pdb=" N LYS A1004 " --> pdb=" O SER A1000 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A1005 " --> pdb=" O ASP A1001 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE A1006 " --> pdb=" O ILE A1002 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU A1007 " --> pdb=" O PHE A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1031 Processing helix chain 'A' and resid 1039 through 1046 removed outlier: 3.760A pdb=" N VAL A1043 " --> pdb=" O ASP A1039 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A1044 " --> pdb=" O GLU A1040 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A1045 " --> pdb=" O ASP A1041 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1039 through 1046' Processing helix chain 'A' and resid 1065 through 1077 removed outlier: 3.575A pdb=" N THR A1069 " --> pdb=" O THR A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1082 Processing helix chain 'A' and resid 1102 through 1104 No H-bonds generated for 'chain 'A' and resid 1102 through 1104' Processing helix chain 'A' and resid 1137 through 1140 No H-bonds generated for 'chain 'A' and resid 1137 through 1140' Processing helix chain 'A' and resid 1143 through 1157 Processing helix chain 'A' and resid 1159 through 1164 Processing helix chain 'A' and resid 1178 through 1183 Processing helix chain 'D' and resid 9 through 17 Processing helix chain 'D' and resid 46 through 50 removed outlier: 3.758A pdb=" N ARG D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 46 through 50' Processing helix chain 'E' and resid 736 through 739 No H-bonds generated for 'chain 'E' and resid 736 through 739' Processing helix chain 'B' and resid 22 through 28 Processing helix chain 'B' and resid 131 through 137 removed outlier: 3.803A pdb=" N MET B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 152 Processing helix chain 'B' and resid 158 through 167 Processing helix chain 'B' and resid 182 through 198 Processing helix chain 'B' and resid 208 through 215 Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 228 through 238 Processing helix chain 'B' and resid 254 through 269 Processing helix chain 'B' and resid 277 through 287 Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 318 through 320 No H-bonds generated for 'chain 'B' and resid 318 through 320' Processing helix chain 'B' and resid 325 through 335 Processing helix chain 'B' and resid 341 through 348 Proline residue: B 346 - end of helix Processing helix chain 'B' and resid 358 through 364 removed outlier: 3.954A pdb=" N LYS B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 272 through 274 removed outlier: 3.911A pdb=" N ARG A 75 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR A 120 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET A 82 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASP A 118 " --> pdb=" O MET A 82 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ALA A 84 " --> pdb=" O GLY A 116 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLY A 116 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU A 86 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ILE A 114 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 137 through 142 Processing sheet with id= C, first strand: chain 'A' and resid 418 through 421 removed outlier: 3.596A pdb=" N THR A 376 " --> pdb=" O MET A 420 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N MET A 309 " --> pdb=" O ASN A 324 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE A 346 " --> pdb=" O GLY A 319 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LEU A 321 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR A 348 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR A 323 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N PHE A 350 " --> pdb=" O THR A 323 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 404 through 406 Processing sheet with id= E, first strand: chain 'A' and resid 558 through 560 removed outlier: 6.945A pdb=" N TRP A 880 " --> pdb=" O LEU A 872 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU A 874 " --> pdb=" O GLY A 878 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLY A 878 " --> pdb=" O LEU A 874 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 564 through 567 removed outlier: 3.584A pdb=" N ALA A 952 " --> pdb=" O PHE A 972 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 980 " --> pdb=" O VAL A 971 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 571 through 575 Processing sheet with id= H, first strand: chain 'A' and resid 678 through 687 Processing sheet with id= I, first strand: chain 'A' and resid 890 through 894 Processing sheet with id= J, first strand: chain 'A' and resid 923 through 928 removed outlier: 6.871A pdb=" N ILE A 933 " --> pdb=" O LYS A 927 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= L, first strand: chain 'D' and resid 71 through 76 Processing sheet with id= M, first strand: chain 'D' and resid 102 through 107 removed outlier: 6.349A pdb=" N HIS D 105 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LEU D 115 " --> pdb=" O HIS D 105 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN D 107 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL D 113 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 3 through 7 removed outlier: 7.586A pdb=" N MET B 96 " --> pdb=" O ASN B 4 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N HIS B 6 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 98 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP B 97 " --> pdb=" O PHE B 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU B 71 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS B 103 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL B 69 " --> pdb=" O LYS B 103 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 38 through 41 removed outlier: 5.398A pdb=" N VAL B 49 " --> pdb=" O LEU B 60 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 170 through 173 Processing sheet with id= Q, first strand: chain 'B' and resid 239 through 241 Processing sheet with id= R, first strand: chain 'B' and resid 367 through 370 470 hydrogen bonds defined for protein. 1338 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: 4.17 Time building geometry restraints manager: 5.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.40: 5172 1.40 - 1.59: 7448 1.59 - 1.78: 8 1.78 - 1.96: 99 1.96 - 2.15: 12 Bond restraints: 12739 Sorted by residual: bond pdb=" S2 SF4 A1401 " pdb="FE4 SF4 A1401 " ideal model delta sigma weight residual 2.280 2.098 0.182 3.00e-02 1.11e+03 3.68e+01 bond pdb=" S4 SF4 A1401 " pdb="FE1 SF4 A1401 " ideal model delta sigma weight residual 2.280 2.100 0.180 3.00e-02 1.11e+03 3.59e+01 bond pdb=" S2 SF4 A1401 " pdb="FE3 SF4 A1401 " ideal model delta sigma weight residual 2.280 2.117 0.163 3.00e-02 1.11e+03 2.95e+01 bond pdb=" S3 SF4 A1401 " pdb="FE2 SF4 A1401 " ideal model delta sigma weight residual 2.280 2.125 0.155 3.00e-02 1.11e+03 2.67e+01 bond pdb=" S4 SF4 A1401 " pdb="FE3 SF4 A1401 " ideal model delta sigma weight residual 2.280 2.126 0.154 3.00e-02 1.11e+03 2.62e+01 ... (remaining 12734 not shown) Histogram of bond angle deviations from ideal: 68.96 - 83.11: 12 83.11 - 97.26: 1 97.26 - 111.41: 5030 111.41 - 125.55: 11905 125.55 - 139.70: 272 Bond angle restraints: 17220 Sorted by residual: angle pdb=" CA GLU A 623 " pdb=" CB GLU A 623 " pdb=" CG GLU A 623 " ideal model delta sigma weight residual 114.10 128.77 -14.67 2.00e+00 2.50e-01 5.38e+01 angle pdb=" CA LEU A1045 " pdb=" CB LEU A1045 " pdb=" CG LEU A1045 " ideal model delta sigma weight residual 116.30 139.70 -23.40 3.50e+00 8.16e-02 4.47e+01 angle pdb=" C GLU A 244 " pdb=" N TYR A 245 " pdb=" CA TYR A 245 " ideal model delta sigma weight residual 122.26 111.53 10.73 1.73e+00 3.34e-01 3.85e+01 angle pdb=" CA LEU B 87 " pdb=" CB LEU B 87 " pdb=" CG LEU B 87 " ideal model delta sigma weight residual 116.30 136.03 -19.73 3.50e+00 8.16e-02 3.18e+01 angle pdb=" C THR B 375 " pdb=" N VAL B 376 " pdb=" CA VAL B 376 " ideal model delta sigma weight residual 122.48 116.28 6.20 1.13e+00 7.83e-01 3.01e+01 ... (remaining 17215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 6970 17.81 - 35.61: 603 35.61 - 53.42: 115 53.42 - 71.23: 27 71.23 - 89.03: 8 Dihedral angle restraints: 7723 sinusoidal: 3214 harmonic: 4509 Sorted by residual: dihedral pdb=" CA SER B 379 " pdb=" C SER B 379 " pdb=" N ARG B 380 " pdb=" CA ARG B 380 " ideal model delta harmonic sigma weight residual -180.00 -135.01 -44.99 0 5.00e+00 4.00e-02 8.10e+01 dihedral pdb=" CA ARG A 663 " pdb=" C ARG A 663 " pdb=" N ASP A 664 " pdb=" CA ASP A 664 " ideal model delta harmonic sigma weight residual 180.00 153.72 26.28 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ARG A 672 " pdb=" C ARG A 672 " pdb=" N PRO A 673 " pdb=" CA PRO A 673 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 7720 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.479: 1892 0.479 - 0.957: 0 0.957 - 1.436: 0 1.436 - 1.914: 0 1.914 - 2.393: 4 Chirality restraints: 1896 Sorted by residual: chirality pdb="FE4 SF4 A1401 " pdb=" S1 SF4 A1401 " pdb=" S2 SF4 A1401 " pdb=" S3 SF4 A1401 " both_signs ideal model delta sigma weight residual False 10.55 8.16 2.39 2.00e-01 2.50e+01 1.43e+02 chirality pdb="FE2 SF4 A1401 " pdb=" S1 SF4 A1401 " pdb=" S3 SF4 A1401 " pdb=" S4 SF4 A1401 " both_signs ideal model delta sigma weight residual False 10.55 8.28 2.28 2.00e-01 2.50e+01 1.30e+02 chirality pdb="FE1 SF4 A1401 " pdb=" S2 SF4 A1401 " pdb=" S3 SF4 A1401 " pdb=" S4 SF4 A1401 " both_signs ideal model delta sigma weight residual False -10.55 -8.39 -2.17 2.00e-01 2.50e+01 1.17e+02 ... (remaining 1893 not shown) Planarity restraints: 2200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 80 " -0.022 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C THR A 80 " 0.074 2.00e-02 2.50e+03 pdb=" O THR A 80 " -0.027 2.00e-02 2.50e+03 pdb=" N ASN A 81 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 863 " 0.021 2.00e-02 2.50e+03 4.27e-02 1.82e+01 pdb=" C ALA A 863 " -0.074 2.00e-02 2.50e+03 pdb=" O ALA A 863 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU A 864 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 762 " -0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C VAL A 762 " 0.072 2.00e-02 2.50e+03 pdb=" O VAL A 762 " -0.028 2.00e-02 2.50e+03 pdb=" N CYS A 763 " -0.024 2.00e-02 2.50e+03 ... (remaining 2197 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1551 2.75 - 3.29: 12243 3.29 - 3.83: 21109 3.83 - 4.36: 24313 4.36 - 4.90: 40304 Nonbonded interactions: 99520 Sorted by model distance: nonbonded pdb=" OH TYR B 261 " pdb=" O TRP B 284 " model vdw 2.218 2.440 nonbonded pdb=" O LYS B 357 " pdb=" OG SER B 360 " model vdw 2.255 2.440 nonbonded pdb=" O TYR A 135 " pdb=" OH TYR A 249 " model vdw 2.263 2.440 nonbonded pdb=" O LEU D 73 " pdb=" OG SER B 2 " model vdw 2.283 2.440 nonbonded pdb=" OG1 THR A1068 " pdb=" O THR A1103 " model vdw 2.296 2.440 ... (remaining 99515 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.62 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.920 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 38.320 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 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 0.182 12739 Z= 0.596 Angle : 1.525 23.403 17220 Z= 0.848 Chirality : 0.129 2.393 1896 Planarity : 0.009 0.088 2200 Dihedral : 14.137 89.031 4799 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.68 % Favored : 95.19 % Rotamer: Outliers : 1.88 % Allowed : 8.38 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.45 (0.19), residues: 1517 helix: -0.89 (0.19), residues: 555 sheet: -0.40 (0.30), residues: 248 loop : -1.11 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP A 78 HIS 0.011 0.003 HIS A 915 PHE 0.058 0.004 PHE B 288 TYR 0.039 0.005 TYR A 245 ARG 0.027 0.002 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 236 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 PHE cc_start: 0.8371 (m-80) cc_final: 0.7938 (m-10) REVERT: A 121 PHE cc_start: 0.8616 (m-80) cc_final: 0.8094 (m-80) REVERT: A 135 TYR cc_start: 0.8095 (t80) cc_final: 0.7468 (t80) REVERT: A 148 ARG cc_start: 0.8115 (mtp180) cc_final: 0.7894 (ptm160) REVERT: A 151 ASP cc_start: 0.7662 (m-30) cc_final: 0.7442 (m-30) REVERT: A 186 LYS cc_start: 0.8642 (tttp) cc_final: 0.8232 (tptt) REVERT: A 314 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8353 (tpp) REVERT: A 383 ASP cc_start: 0.7583 (m-30) cc_final: 0.6704 (m-30) REVERT: A 453 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8337 (tp30) REVERT: A 459 MET cc_start: 0.7464 (mtt) cc_final: 0.6782 (mtt) REVERT: A 811 LYS cc_start: 0.8802 (mttp) cc_final: 0.8497 (mttt) REVERT: A 827 LEU cc_start: 0.9539 (tt) cc_final: 0.9319 (tt) REVERT: A 955 LEU cc_start: 0.8945 (mp) cc_final: 0.8693 (mp) REVERT: A 1146 TYR cc_start: 0.8871 (m-80) cc_final: 0.8488 (m-10) REVERT: D 78 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6722 (tm-30) REVERT: D 81 THR cc_start: 0.7944 (OUTLIER) cc_final: 0.7671 (t) REVERT: D 109 LYS cc_start: 0.8376 (mmmt) cc_final: 0.8091 (mmmt) REVERT: D 117 ASP cc_start: 0.8615 (t0) cc_final: 0.8332 (t0) REVERT: B 16 LYS cc_start: 0.8870 (mttm) cc_final: 0.8595 (mmpt) REVERT: B 232 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8652 (pt0) REVERT: B 236 ASN cc_start: 0.8921 (m-40) cc_final: 0.8382 (p0) REVERT: B 295 ASP cc_start: 0.7767 (p0) cc_final: 0.7547 (p0) outliers start: 26 outliers final: 9 residues processed: 257 average time/residue: 0.2660 time to fit residues: 96.2456 Evaluate side-chains 175 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 164 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 88 optimal weight: 0.2980 chunk 138 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 444 GLN A 450 ASN A 490 HIS A 671 ASN A 973 ASN A 999 GLN ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12739 Z= 0.204 Angle : 0.682 8.998 17220 Z= 0.354 Chirality : 0.045 0.191 1896 Planarity : 0.005 0.049 2200 Dihedral : 5.322 39.047 1661 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.22 % Allowed : 2.31 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -0.16 (0.21), residues: 1517 helix: 0.64 (0.21), residues: 558 sheet: -0.06 (0.32), residues: 250 loop : -0.64 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 841 HIS 0.004 0.001 HIS A 394 PHE 0.022 0.002 PHE B 288 TYR 0.033 0.002 TYR A 412 ARG 0.007 0.001 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 200 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 PHE cc_start: 0.8303 (m-80) cc_final: 0.7722 (m-10) REVERT: A 121 PHE cc_start: 0.8697 (m-80) cc_final: 0.8103 (m-80) REVERT: A 135 TYR cc_start: 0.8009 (t80) cc_final: 0.7367 (t80) REVERT: A 186 LYS cc_start: 0.8461 (tttp) cc_final: 0.8036 (tptt) REVERT: A 452 ILE cc_start: 0.7853 (tp) cc_final: 0.7180 (pt) REVERT: A 459 MET cc_start: 0.7605 (mtt) cc_final: 0.6904 (mtt) REVERT: A 517 GLU cc_start: 0.8718 (tt0) cc_final: 0.8497 (tm-30) REVERT: A 1023 CYS cc_start: 0.7992 (t) cc_final: 0.7734 (t) REVERT: A 1036 MET cc_start: 0.4500 (mmp) cc_final: 0.4238 (tpt) REVERT: A 1146 TYR cc_start: 0.8685 (m-80) cc_final: 0.8325 (m-10) REVERT: A 1165 GLN cc_start: 0.7751 (mp10) cc_final: 0.7543 (tm-30) REVERT: D 30 MET cc_start: 0.7714 (mmm) cc_final: 0.7057 (mmt) REVERT: D 109 LYS cc_start: 0.8366 (mmmt) cc_final: 0.8051 (mmmt) REVERT: D 117 ASP cc_start: 0.8621 (t0) cc_final: 0.8361 (t0) REVERT: D 119 MET cc_start: 0.8731 (mmp) cc_final: 0.8379 (mmm) REVERT: B 72 MET cc_start: 0.8475 (mpp) cc_final: 0.8196 (mpp) REVERT: B 232 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8840 (mt-10) REVERT: B 295 ASP cc_start: 0.7810 (p0) cc_final: 0.7603 (p0) outliers start: 3 outliers final: 0 residues processed: 202 average time/residue: 0.2452 time to fit residues: 71.8239 Evaluate side-chains 147 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 149 optimal weight: 0.0010 chunk 123 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN B 212 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12739 Z= 0.174 Angle : 0.595 7.151 17220 Z= 0.307 Chirality : 0.043 0.168 1896 Planarity : 0.004 0.042 2200 Dihedral : 4.907 27.447 1661 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 0.12 (0.21), residues: 1517 helix: 0.88 (0.21), residues: 561 sheet: -0.01 (0.31), residues: 270 loop : -0.45 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 284 HIS 0.004 0.001 HIS A 365 PHE 0.016 0.001 PHE B 288 TYR 0.025 0.002 TYR A 412 ARG 0.005 0.000 ARG A1147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8471 (m-30) cc_final: 0.8268 (m-30) REVERT: A 52 PHE cc_start: 0.8191 (m-80) cc_final: 0.7756 (m-10) REVERT: A 121 PHE cc_start: 0.8820 (m-80) cc_final: 0.8188 (m-80) REVERT: A 148 ARG cc_start: 0.8072 (mtp180) cc_final: 0.7861 (ptm160) REVERT: A 186 LYS cc_start: 0.8433 (tttp) cc_final: 0.8123 (tptt) REVERT: A 459 MET cc_start: 0.7491 (mtt) cc_final: 0.6945 (mtt) REVERT: A 505 ASP cc_start: 0.8427 (m-30) cc_final: 0.8179 (m-30) REVERT: A 517 GLU cc_start: 0.8746 (tt0) cc_final: 0.8306 (tm-30) REVERT: A 521 MET cc_start: 0.9196 (mtt) cc_final: 0.7848 (mtt) REVERT: A 1036 MET cc_start: 0.4637 (mmp) cc_final: 0.4339 (tpt) REVERT: A 1146 TYR cc_start: 0.8726 (m-80) cc_final: 0.8240 (m-10) REVERT: A 1165 GLN cc_start: 0.7852 (mp10) cc_final: 0.7632 (tm-30) REVERT: D 30 MET cc_start: 0.7922 (mmm) cc_final: 0.7165 (mmm) REVERT: D 117 ASP cc_start: 0.8636 (t0) cc_final: 0.8117 (t0) REVERT: D 119 MET cc_start: 0.8669 (mmp) cc_final: 0.7947 (mmp) REVERT: B 72 MET cc_start: 0.8550 (mpp) cc_final: 0.8315 (mpp) REVERT: B 232 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8815 (mt-10) REVERT: B 295 ASP cc_start: 0.7747 (p0) cc_final: 0.7526 (p0) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2317 time to fit residues: 62.4520 Evaluate side-chains 146 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 65 optimal weight: 0.1980 chunk 92 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 146 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 HIS ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12739 Z= 0.144 Angle : 0.569 7.985 17220 Z= 0.289 Chirality : 0.042 0.164 1896 Planarity : 0.004 0.041 2200 Dihedral : 4.699 23.667 1661 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 0.25 (0.21), residues: 1517 helix: 0.92 (0.21), residues: 560 sheet: 0.08 (0.31), residues: 269 loop : -0.33 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 284 HIS 0.003 0.001 HIS A 83 PHE 0.015 0.001 PHE A 998 TYR 0.022 0.001 TYR A 412 ARG 0.003 0.000 ARG D 89 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 PHE cc_start: 0.8082 (m-80) cc_final: 0.7851 (m-10) REVERT: A 135 TYR cc_start: 0.7582 (t80) cc_final: 0.7082 (t80) REVERT: A 186 LYS cc_start: 0.8456 (tttp) cc_final: 0.8149 (tptt) REVERT: A 452 ILE cc_start: 0.7524 (tp) cc_final: 0.7082 (pt) REVERT: A 459 MET cc_start: 0.7417 (mtt) cc_final: 0.6899 (mtt) REVERT: A 483 TYR cc_start: 0.8625 (m-80) cc_final: 0.8321 (m-10) REVERT: A 517 GLU cc_start: 0.8665 (tt0) cc_final: 0.8400 (tm-30) REVERT: A 521 MET cc_start: 0.9256 (mtt) cc_final: 0.8517 (mmt) REVERT: A 808 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7739 (tp30) REVERT: A 953 MET cc_start: 0.8315 (tpp) cc_final: 0.7998 (mmm) REVERT: A 1036 MET cc_start: 0.4679 (mmp) cc_final: 0.4209 (tpt) REVERT: A 1146 TYR cc_start: 0.8726 (m-80) cc_final: 0.8235 (m-10) REVERT: D 119 MET cc_start: 0.8632 (mmp) cc_final: 0.7911 (mmm) REVERT: B 51 LEU cc_start: 0.8946 (tp) cc_final: 0.8675 (tp) REVERT: B 136 MET cc_start: 0.7514 (mmt) cc_final: 0.7268 (mmp) REVERT: B 194 MET cc_start: 0.8975 (mtm) cc_final: 0.8728 (mtt) REVERT: B 232 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8795 (mt-10) REVERT: B 295 ASP cc_start: 0.7790 (p0) cc_final: 0.7563 (p0) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2227 time to fit residues: 63.6766 Evaluate side-chains 148 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 37 optimal weight: 0.0570 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 GLN ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12739 Z= 0.145 Angle : 0.562 7.353 17220 Z= 0.284 Chirality : 0.042 0.162 1896 Planarity : 0.004 0.040 2200 Dihedral : 4.548 24.157 1661 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 0.28 (0.21), residues: 1517 helix: 0.96 (0.22), residues: 559 sheet: 0.10 (0.31), residues: 265 loop : -0.32 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 284 HIS 0.005 0.001 HIS A 490 PHE 0.022 0.001 PHE B 288 TYR 0.017 0.001 TYR A 412 ARG 0.007 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 PHE cc_start: 0.8111 (m-80) cc_final: 0.7847 (m-10) REVERT: A 121 PHE cc_start: 0.8718 (m-80) cc_final: 0.8058 (m-80) REVERT: A 135 TYR cc_start: 0.7571 (t80) cc_final: 0.7040 (t80) REVERT: A 148 ARG cc_start: 0.6809 (ppt170) cc_final: 0.6369 (ptm160) REVERT: A 186 LYS cc_start: 0.8462 (tttp) cc_final: 0.8160 (tptt) REVERT: A 314 MET cc_start: 0.8806 (tpp) cc_final: 0.8576 (tpt) REVERT: A 459 MET cc_start: 0.7096 (mtt) cc_final: 0.6843 (mtt) REVERT: A 483 TYR cc_start: 0.8603 (m-80) cc_final: 0.8344 (m-10) REVERT: A 517 GLU cc_start: 0.8781 (tt0) cc_final: 0.8415 (tm-30) REVERT: A 521 MET cc_start: 0.9349 (mtt) cc_final: 0.8560 (mmt) REVERT: A 808 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7047 (pm20) REVERT: A 835 MET cc_start: 0.9079 (mpp) cc_final: 0.8854 (mpp) REVERT: A 1036 MET cc_start: 0.4473 (mmp) cc_final: 0.4164 (tpt) REVERT: A 1146 TYR cc_start: 0.8728 (m-80) cc_final: 0.8225 (m-10) REVERT: D 114 GLU cc_start: 0.7972 (mp0) cc_final: 0.7765 (mp0) REVERT: B 136 MET cc_start: 0.7486 (mmt) cc_final: 0.7261 (mmp) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2268 time to fit residues: 64.0407 Evaluate side-chains 146 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 HIS A 937 HIS ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12739 Z= 0.283 Angle : 0.653 7.282 17220 Z= 0.338 Chirality : 0.044 0.180 1896 Planarity : 0.005 0.051 2200 Dihedral : 4.896 24.200 1661 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 0.04 (0.21), residues: 1517 helix: 0.74 (0.21), residues: 561 sheet: 0.05 (0.31), residues: 261 loop : -0.48 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 284 HIS 0.006 0.001 HIS A 83 PHE 0.018 0.002 PHE A 121 TYR 0.028 0.002 TYR A 770 ARG 0.010 0.001 ARG A 780 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8507 (m-30) cc_final: 0.8228 (m-30) REVERT: A 52 PHE cc_start: 0.8225 (m-80) cc_final: 0.7876 (m-10) REVERT: A 121 PHE cc_start: 0.8839 (m-80) cc_final: 0.8022 (m-80) REVERT: A 135 TYR cc_start: 0.7739 (t80) cc_final: 0.7233 (t80) REVERT: A 186 LYS cc_start: 0.8666 (tttp) cc_final: 0.8358 (tptt) REVERT: A 415 SER cc_start: 0.8403 (p) cc_final: 0.7706 (p) REVERT: A 459 MET cc_start: 0.7402 (mtt) cc_final: 0.6887 (mtt) REVERT: A 517 GLU cc_start: 0.8851 (tt0) cc_final: 0.8271 (tm-30) REVERT: A 521 MET cc_start: 0.9422 (mtt) cc_final: 0.8163 (mtt) REVERT: A 879 ILE cc_start: 0.9343 (mt) cc_final: 0.9090 (mm) REVERT: A 1036 MET cc_start: 0.4777 (mmp) cc_final: 0.4474 (tpt) REVERT: A 1146 TYR cc_start: 0.8554 (m-80) cc_final: 0.8043 (m-10) REVERT: D 30 MET cc_start: 0.6972 (mmm) cc_final: 0.6543 (mmm) REVERT: D 32 MET cc_start: 0.8346 (pmm) cc_final: 0.8013 (pmm) REVERT: D 117 ASP cc_start: 0.8332 (t0) cc_final: 0.7962 (t0) REVERT: D 119 MET cc_start: 0.8495 (mmp) cc_final: 0.7794 (mmm) REVERT: B 72 MET cc_start: 0.8941 (mpp) cc_final: 0.8526 (mpp) REVERT: B 136 MET cc_start: 0.7537 (mmt) cc_final: 0.7325 (mmp) REVERT: B 232 GLU cc_start: 0.9102 (pt0) cc_final: 0.8782 (pp20) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2366 time to fit residues: 62.6068 Evaluate side-chains 138 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.6980 chunk 16 optimal weight: 0.0770 chunk 83 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.2740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 HIS ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12739 Z= 0.169 Angle : 0.582 9.975 17220 Z= 0.296 Chirality : 0.042 0.155 1896 Planarity : 0.004 0.040 2200 Dihedral : 4.685 26.047 1661 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 0.22 (0.21), residues: 1517 helix: 1.02 (0.22), residues: 551 sheet: 0.00 (0.31), residues: 256 loop : -0.41 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 841 HIS 0.004 0.001 HIS A 490 PHE 0.019 0.001 PHE B 288 TYR 0.018 0.001 TYR A 245 ARG 0.006 0.000 ARG A 840 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8503 (m-30) cc_final: 0.8171 (m-30) REVERT: A 52 PHE cc_start: 0.8220 (m-80) cc_final: 0.7828 (m-10) REVERT: A 121 PHE cc_start: 0.8772 (m-80) cc_final: 0.8073 (m-80) REVERT: A 135 TYR cc_start: 0.7647 (t80) cc_final: 0.7190 (t80) REVERT: A 148 ARG cc_start: 0.6550 (ppt170) cc_final: 0.6051 (ptm160) REVERT: A 186 LYS cc_start: 0.8677 (tttp) cc_final: 0.8215 (tptp) REVERT: A 415 SER cc_start: 0.8240 (p) cc_final: 0.7469 (p) REVERT: A 459 MET cc_start: 0.7304 (mtt) cc_final: 0.6682 (mtt) REVERT: A 517 GLU cc_start: 0.8716 (tt0) cc_final: 0.8261 (tm-30) REVERT: A 521 MET cc_start: 0.9358 (mtt) cc_final: 0.8278 (mtt) REVERT: A 835 MET cc_start: 0.9241 (mpp) cc_final: 0.8971 (mpp) REVERT: A 879 ILE cc_start: 0.9263 (mt) cc_final: 0.9006 (mm) REVERT: A 1036 MET cc_start: 0.4638 (mmp) cc_final: 0.4299 (tpt) REVERT: A 1146 TYR cc_start: 0.8700 (m-80) cc_final: 0.8221 (m-10) REVERT: D 30 MET cc_start: 0.7090 (mmm) cc_final: 0.6535 (mmm) REVERT: D 117 ASP cc_start: 0.8282 (t0) cc_final: 0.7868 (t0) REVERT: D 119 MET cc_start: 0.8509 (mmp) cc_final: 0.7739 (mmm) REVERT: B 51 LEU cc_start: 0.8950 (tp) cc_final: 0.8677 (tp) REVERT: B 72 MET cc_start: 0.8890 (mpp) cc_final: 0.8575 (mpp) REVERT: B 232 GLU cc_start: 0.9104 (pt0) cc_final: 0.8728 (pp20) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2215 time to fit residues: 58.0839 Evaluate side-chains 143 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 99 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12739 Z= 0.158 Angle : 0.578 9.184 17220 Z= 0.293 Chirality : 0.042 0.152 1896 Planarity : 0.004 0.041 2200 Dihedral : 4.551 23.718 1661 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 0.27 (0.21), residues: 1517 helix: 1.05 (0.22), residues: 556 sheet: -0.03 (0.31), residues: 262 loop : -0.36 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 841 HIS 0.003 0.001 HIS A 490 PHE 0.027 0.001 PHE D 45 TYR 0.019 0.001 TYR A 249 ARG 0.006 0.000 ARG A 780 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8338 (m-30) cc_final: 0.8050 (m-30) REVERT: A 52 PHE cc_start: 0.8148 (m-80) cc_final: 0.7770 (m-10) REVERT: A 135 TYR cc_start: 0.7597 (t80) cc_final: 0.7157 (t80) REVERT: A 186 LYS cc_start: 0.8641 (tttp) cc_final: 0.8242 (tptt) REVERT: A 193 PHE cc_start: 0.7176 (m-10) cc_final: 0.6615 (m-10) REVERT: A 415 SER cc_start: 0.8267 (p) cc_final: 0.7460 (p) REVERT: A 459 MET cc_start: 0.7228 (mtt) cc_final: 0.6673 (mtt) REVERT: A 483 TYR cc_start: 0.8649 (m-80) cc_final: 0.8394 (m-10) REVERT: A 517 GLU cc_start: 0.8755 (tt0) cc_final: 0.8283 (tm-30) REVERT: A 521 MET cc_start: 0.9202 (mtt) cc_final: 0.8408 (mmt) REVERT: A 657 ASP cc_start: 0.7971 (p0) cc_final: 0.7527 (p0) REVERT: A 835 MET cc_start: 0.9217 (mpp) cc_final: 0.8968 (mpp) REVERT: A 1146 TYR cc_start: 0.8712 (m-80) cc_final: 0.8245 (m-10) REVERT: D 30 MET cc_start: 0.7327 (mmm) cc_final: 0.6673 (mmm) REVERT: D 119 MET cc_start: 0.8496 (mmp) cc_final: 0.7955 (mmm) REVERT: B 72 MET cc_start: 0.8802 (mpp) cc_final: 0.8446 (mpp) REVERT: B 232 GLU cc_start: 0.9110 (pt0) cc_final: 0.8739 (pp20) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2193 time to fit residues: 57.2384 Evaluate side-chains 144 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12739 Z= 0.178 Angle : 0.589 8.171 17220 Z= 0.300 Chirality : 0.043 0.171 1896 Planarity : 0.004 0.042 2200 Dihedral : 4.565 26.294 1661 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 0.25 (0.21), residues: 1517 helix: 1.00 (0.22), residues: 550 sheet: -0.06 (0.30), residues: 262 loop : -0.32 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 284 HIS 0.003 0.001 HIS A 83 PHE 0.028 0.001 PHE A 594 TYR 0.019 0.001 TYR A 249 ARG 0.008 0.000 ARG A1173 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8493 (m-30) cc_final: 0.8166 (m-30) REVERT: A 52 PHE cc_start: 0.8202 (m-80) cc_final: 0.7767 (m-10) REVERT: A 121 PHE cc_start: 0.8730 (m-80) cc_final: 0.7998 (m-80) REVERT: A 135 TYR cc_start: 0.7619 (t80) cc_final: 0.7156 (t80) REVERT: A 186 LYS cc_start: 0.8661 (tttp) cc_final: 0.8054 (tptt) REVERT: A 193 PHE cc_start: 0.7248 (m-10) cc_final: 0.6741 (m-10) REVERT: A 415 SER cc_start: 0.8331 (p) cc_final: 0.7538 (p) REVERT: A 459 MET cc_start: 0.7251 (mtt) cc_final: 0.6719 (mtt) REVERT: A 517 GLU cc_start: 0.8804 (tt0) cc_final: 0.8335 (tm-30) REVERT: A 521 MET cc_start: 0.9315 (mtt) cc_final: 0.8529 (mmt) REVERT: A 657 ASP cc_start: 0.8046 (p0) cc_final: 0.7583 (p0) REVERT: A 835 MET cc_start: 0.9192 (mpp) cc_final: 0.8976 (mpp) REVERT: A 1146 TYR cc_start: 0.8702 (m-80) cc_final: 0.8237 (m-10) REVERT: D 30 MET cc_start: 0.7406 (mmm) cc_final: 0.6786 (mmm) REVERT: D 32 MET cc_start: 0.8531 (pmm) cc_final: 0.8203 (pmm) REVERT: B 51 LEU cc_start: 0.8948 (tp) cc_final: 0.8641 (tp) REVERT: B 72 MET cc_start: 0.8892 (mpp) cc_final: 0.8546 (mpp) REVERT: B 232 GLU cc_start: 0.9146 (pt0) cc_final: 0.8735 (pp20) REVERT: B 323 MET cc_start: 0.8367 (mmm) cc_final: 0.8046 (mmm) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2211 time to fit residues: 58.3186 Evaluate side-chains 139 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 139 optimal weight: 0.0070 chunk 120 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 73 optimal weight: 0.0980 chunk 95 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12739 Z= 0.152 Angle : 0.574 8.206 17220 Z= 0.292 Chirality : 0.043 0.165 1896 Planarity : 0.004 0.042 2200 Dihedral : 4.497 28.813 1661 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: 0.32 (0.22), residues: 1517 helix: 1.06 (0.22), residues: 549 sheet: -0.06 (0.29), residues: 283 loop : -0.25 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 284 HIS 0.006 0.001 HIS A 490 PHE 0.021 0.001 PHE A 777 TYR 0.016 0.001 TYR B 261 ARG 0.009 0.000 ARG A1173 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8336 (m-30) cc_final: 0.7991 (m-30) REVERT: A 52 PHE cc_start: 0.8130 (m-80) cc_final: 0.7703 (m-10) REVERT: A 121 PHE cc_start: 0.8676 (m-80) cc_final: 0.7939 (m-80) REVERT: A 135 TYR cc_start: 0.7581 (t80) cc_final: 0.7114 (t80) REVERT: A 186 LYS cc_start: 0.8654 (tttp) cc_final: 0.8059 (tptt) REVERT: A 193 PHE cc_start: 0.7260 (m-10) cc_final: 0.6801 (m-10) REVERT: A 314 MET cc_start: 0.9003 (tpt) cc_final: 0.8745 (tpt) REVERT: A 415 SER cc_start: 0.8217 (p) cc_final: 0.7357 (p) REVERT: A 459 MET cc_start: 0.7309 (mtt) cc_final: 0.6735 (mtt) REVERT: A 517 GLU cc_start: 0.8788 (tt0) cc_final: 0.8288 (tm-30) REVERT: A 521 MET cc_start: 0.9326 (mtt) cc_final: 0.8545 (mmt) REVERT: A 657 ASP cc_start: 0.7989 (p0) cc_final: 0.7496 (p0) REVERT: A 808 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7158 (mp0) REVERT: A 811 LYS cc_start: 0.8968 (pttm) cc_final: 0.8757 (pttm) REVERT: A 835 MET cc_start: 0.9210 (mpp) cc_final: 0.8977 (mpp) REVERT: A 1083 LYS cc_start: 0.6476 (tppt) cc_final: 0.5559 (ttpt) REVERT: A 1146 TYR cc_start: 0.8730 (m-80) cc_final: 0.8253 (m-10) REVERT: D 30 MET cc_start: 0.7373 (mmm) cc_final: 0.6689 (mmm) REVERT: D 32 MET cc_start: 0.8397 (pmm) cc_final: 0.8084 (pmm) REVERT: B 51 LEU cc_start: 0.8918 (tp) cc_final: 0.8681 (tp) REVERT: B 72 MET cc_start: 0.8918 (mpp) cc_final: 0.8462 (mpp) REVERT: B 232 GLU cc_start: 0.9180 (pt0) cc_final: 0.8741 (pp20) REVERT: B 284 TRP cc_start: 0.8016 (t60) cc_final: 0.7736 (t60) REVERT: B 323 MET cc_start: 0.8338 (mmm) cc_final: 0.8008 (mmm) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2210 time to fit residues: 59.1509 Evaluate side-chains 149 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.081093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.065753 restraints weight = 66548.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.067225 restraints weight = 43608.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.068201 restraints weight = 32611.048| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12739 Z= 0.227 Angle : 0.629 8.792 17220 Z= 0.322 Chirality : 0.043 0.162 1896 Planarity : 0.004 0.042 2200 Dihedral : 4.735 33.109 1661 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.21 (0.22), residues: 1517 helix: 0.97 (0.22), residues: 548 sheet: -0.17 (0.30), residues: 282 loop : -0.29 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 284 HIS 0.004 0.001 HIS A 83 PHE 0.021 0.002 PHE A 777 TYR 0.020 0.002 TYR A 249 ARG 0.008 0.001 ARG A1173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2464.28 seconds wall clock time: 45 minutes 22.74 seconds (2722.74 seconds total)