Starting phenix.real_space_refine on Wed Apr 10 20:41:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rmg_4936/04_2024/6rmg_4936_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rmg_4936/04_2024/6rmg_4936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rmg_4936/04_2024/6rmg_4936.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rmg_4936/04_2024/6rmg_4936.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rmg_4936/04_2024/6rmg_4936_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rmg_4936/04_2024/6rmg_4936_trim.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 784 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 50 5.16 5 C 6442 2.51 5 N 1556 2.21 5 O 1761 1.98 5 H 9327 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 85": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 138": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 144": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 255": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 441": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 602": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 824": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 893": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 960": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 962": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 982": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 1113": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1114": not complete - not flipped Residue "B ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19137 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 16284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 16284 Classifications: {'peptide': 1026} Link IDs: {'CIS': 2, 'PTRANS': 45, 'TRANS': 978} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 2369 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 455 Unusual residues: {'NAG': 5, 'Y01': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.10, per 1000 atoms: 0.48 Number of scatterers: 19137 At special positions: 0 Unit cell: (91.9933, 126.186, 140.025, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 50 16.00 O 1761 8.00 N 1556 7.00 C 6442 6.00 H 9327 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 327 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 304 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A1801 " - " ASN A 312 " " NAG A1802 " - " ASN A 349 " " NAG A1803 " - " ASN A 414 " " NAG A1804 " - " ASN A 875 " " NAG A1807 " - " ASN A 141 " " NAG C 1 " - " ASN A1000 " Time building additional restraints: 15.70 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" NE2 HIS B 140 " pdb="ZN ZN B 201 " - pdb=" ND1 HIS B 182 " 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2204 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 6 sheets defined 58.7% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.589A pdb=" N ALA A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 97 removed outlier: 3.730A pdb=" N LEU A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 114 Processing helix chain 'A' and resid 115 through 119 removed outlier: 3.895A pdb=" N ALA A 118 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.803A pdb=" N TRP A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 147 Processing helix chain 'A' and resid 171 through 187 Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.812A pdb=" N LEU A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 Processing helix chain 'A' and resid 230 through 234 Processing helix chain 'A' and resid 235 through 242 Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.698A pdb=" N PHE A 259 " --> pdb=" O TRP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.529A pdb=" N ILE A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 289 through 294 removed outlier: 3.780A pdb=" N ASP A 293 " --> pdb=" O HIS A 289 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 289 through 294' Processing helix chain 'A' and resid 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 388 through 409 removed outlier: 4.018A pdb=" N ALA A 392 " --> pdb=" O ASN A 388 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 438 through 458 Processing helix chain 'A' and resid 466 through 491 removed outlier: 3.636A pdb=" N LEU A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 514 through 524 removed outlier: 3.827A pdb=" N LEU A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 544 removed outlier: 3.612A pdb=" N GLU A 539 " --> pdb=" O ASP A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 554 removed outlier: 3.581A pdb=" N ALA A 549 " --> pdb=" O GLY A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 562 Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'A' and resid 575 through 591 removed outlier: 3.583A pdb=" N LEU A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 605 Processing helix chain 'A' and resid 731 through 739 Processing helix chain 'A' and resid 740 through 745 removed outlier: 3.644A pdb=" N LEU A 744 " --> pdb=" O TYR A 740 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 745 " --> pdb=" O ALA A 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 740 through 745' Processing helix chain 'A' and resid 746 through 770 removed outlier: 4.369A pdb=" N LEU A 761 " --> pdb=" O PHE A 757 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 769 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 770 " --> pdb=" O TYR A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 797 Processing helix chain 'A' and resid 811 through 814 Processing helix chain 'A' and resid 815 through 826 Processing helix chain 'A' and resid 827 through 829 No H-bonds generated for 'chain 'A' and resid 827 through 829' Processing helix chain 'A' and resid 843 through 864 removed outlier: 3.742A pdb=" N GLU A 864 " --> pdb=" O ASP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 888 removed outlier: 3.735A pdb=" N ALA A 883 " --> pdb=" O ASP A 879 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 888 " --> pdb=" O TYR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 902 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.501A pdb=" N GLY A 912 " --> pdb=" O ASP A 909 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE A 913 " --> pdb=" O ALA A 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 909 through 913' Processing helix chain 'A' and resid 918 through 930 Processing helix chain 'A' and resid 930 through 937 Processing helix chain 'A' and resid 983 through 1005 removed outlier: 3.648A pdb=" N LEU A1004 " --> pdb=" O ASN A1000 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A1005 " --> pdb=" O TYR A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1017 removed outlier: 3.502A pdb=" N LEU A1016 " --> pdb=" O GLY A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1020 No H-bonds generated for 'chain 'A' and resid 1018 through 1020' Processing helix chain 'A' and resid 1023 through 1048 removed outlier: 3.645A pdb=" N SER A1033 " --> pdb=" O LEU A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1075 removed outlier: 3.545A pdb=" N GLY A1075 " --> pdb=" O MET A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1103 removed outlier: 3.639A pdb=" N VAL A1084 " --> pdb=" O ALA A1080 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLU A1095 " --> pdb=" O GLY A1091 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE A1096 " --> pdb=" O ILE A1092 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS A1099 " --> pdb=" O GLU A1095 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL A1100 " --> pdb=" O PHE A1096 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA A1101 " --> pdb=" O THR A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1121 removed outlier: 3.602A pdb=" N HIS A1121 " --> pdb=" O LEU A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1138 Processing helix chain 'A' and resid 1139 through 1141 No H-bonds generated for 'chain 'A' and resid 1139 through 1141' Processing helix chain 'A' and resid 1152 through 1168 Processing helix chain 'A' and resid 1169 through 1178 removed outlier: 3.925A pdb=" N VAL A1173 " --> pdb=" O VAL A1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 99 through 114 Processing helix chain 'B' and resid 138 through 143 removed outlier: 4.135A pdb=" N GLU B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 156 No H-bonds generated for 'chain 'B' and resid 154 through 156' Processing helix chain 'B' and resid 157 through 169 Processing sheet with id=AA1, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA3, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 349 removed outlier: 7.199A pdb=" N VAL A 347 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 972 through 978 removed outlier: 3.661A pdb=" N ALA A 972 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A 803 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 804 " --> pdb=" O ASN A1011 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER A1007 " --> pdb=" O GLN A 808 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 86 removed outlier: 6.844A pdb=" N ASP B 147 " --> pdb=" O THR B 125 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1332 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: 6.46 Time building geometry restraints manager: 16.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9311 1.03 - 1.22: 29 1.22 - 1.42: 4095 1.42 - 1.61: 5854 1.61 - 1.81: 109 Bond restraints: 19398 Sorted by residual: bond pdb=" CAE Y01 A1814 " pdb=" CBI Y01 A1814 " ideal model delta sigma weight residual 1.532 1.673 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" CAE Y01 A1813 " pdb=" CBI Y01 A1813 " ideal model delta sigma weight residual 1.532 1.666 -0.134 2.00e-02 2.50e+03 4.51e+01 bond pdb=" CAE Y01 A1817 " pdb=" CBI Y01 A1817 " ideal model delta sigma weight residual 1.532 1.664 -0.132 2.00e-02 2.50e+03 4.34e+01 bond pdb=" CAE Y01 A1811 " pdb=" CBI Y01 A1811 " ideal model delta sigma weight residual 1.532 1.663 -0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" CAV Y01 A1817 " pdb=" CBC Y01 A1817 " ideal model delta sigma weight residual 1.523 1.645 -0.122 2.00e-02 2.50e+03 3.70e+01 ... (remaining 19393 not shown) Histogram of bond angle deviations from ideal: 90.20 - 98.97: 36 98.97 - 107.73: 2712 107.73 - 116.50: 22130 116.50 - 125.26: 9503 125.26 - 134.03: 531 Bond angle restraints: 34912 Sorted by residual: angle pdb=" CAM Y01 A1813 " pdb=" CAY Y01 A1813 " pdb=" OAW Y01 A1813 " ideal model delta sigma weight residual 111.19 127.49 -16.30 3.00e+00 1.11e-01 2.95e+01 angle pdb=" CAM Y01 A1818 " pdb=" CAY Y01 A1818 " pdb=" OAW Y01 A1818 " ideal model delta sigma weight residual 111.19 127.48 -16.29 3.00e+00 1.11e-01 2.95e+01 angle pdb=" CAM Y01 A1808 " pdb=" CAY Y01 A1808 " pdb=" OAW Y01 A1808 " ideal model delta sigma weight residual 111.19 127.43 -16.24 3.00e+00 1.11e-01 2.93e+01 angle pdb=" CAM Y01 A1809 " pdb=" CAY Y01 A1809 " pdb=" OAW Y01 A1809 " ideal model delta sigma weight residual 111.19 127.35 -16.16 3.00e+00 1.11e-01 2.90e+01 angle pdb=" CAM Y01 A1810 " pdb=" CAY Y01 A1810 " pdb=" OAW Y01 A1810 " ideal model delta sigma weight residual 111.19 127.33 -16.14 3.00e+00 1.11e-01 2.90e+01 ... (remaining 34907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 9578 35.97 - 71.94: 227 71.94 - 107.92: 15 107.92 - 143.89: 0 143.89 - 179.86: 1 Dihedral angle restraints: 9821 sinusoidal: 5674 harmonic: 4147 Sorted by residual: dihedral pdb=" CD ARG A1114 " pdb=" NE ARG A1114 " pdb=" CZ ARG A1114 " pdb=" NH1 ARG A1114 " ideal model delta sinusoidal sigma weight residual 0.00 179.86 -179.86 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA ALA A 75 " pdb=" C ALA A 75 " pdb=" N PRO A 76 " pdb=" CA PRO A 76 " ideal model delta harmonic sigma weight residual 180.00 136.27 43.73 0 5.00e+00 4.00e-02 7.65e+01 dihedral pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " pdb=" SG CYS A 304 " pdb=" CB CYS A 304 " ideal model delta sinusoidal sigma weight residual 93.00 168.12 -75.12 1 1.00e+01 1.00e-02 7.14e+01 ... (remaining 9818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1472 0.103 - 0.206: 76 0.206 - 0.308: 10 0.308 - 0.411: 13 0.411 - 0.514: 11 Chirality restraints: 1582 Sorted by residual: chirality pdb=" CBG Y01 A1816 " pdb=" CAQ Y01 A1816 " pdb=" CBD Y01 A1816 " pdb=" CBI Y01 A1816 " both_signs ideal model delta sigma weight residual False -2.33 -2.85 0.51 2.00e-01 2.50e+01 6.60e+00 chirality pdb=" CBG Y01 A1813 " pdb=" CAQ Y01 A1813 " pdb=" CBD Y01 A1813 " pdb=" CBI Y01 A1813 " both_signs ideal model delta sigma weight residual False -2.33 -2.84 0.51 2.00e-01 2.50e+01 6.49e+00 chirality pdb=" CBG Y01 A1810 " pdb=" CAQ Y01 A1810 " pdb=" CBD Y01 A1810 " pdb=" CBI Y01 A1810 " both_signs ideal model delta sigma weight residual False -2.33 -2.83 0.50 2.00e-01 2.50e+01 6.33e+00 ... (remaining 1579 not shown) Planarity restraints: 2799 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 310 " 0.237 2.00e-02 2.50e+03 3.16e-01 1.50e+03 pdb=" CG ASN A 310 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 310 " -0.231 2.00e-02 2.50e+03 pdb=" ND2 ASN A 310 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 310 " -0.486 2.00e-02 2.50e+03 pdb="HD22 ASN A 310 " 0.504 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 915 " 0.216 2.00e-02 2.50e+03 2.66e-01 1.06e+03 pdb=" CG ASN A 915 " -0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN A 915 " -0.215 2.00e-02 2.50e+03 pdb=" ND2 ASN A 915 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN A 915 " -0.408 2.00e-02 2.50e+03 pdb="HD22 ASN A 915 " 0.407 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 417 " -0.186 2.00e-02 2.50e+03 2.08e-01 6.46e+02 pdb=" CD GLN A 417 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLN A 417 " 0.171 2.00e-02 2.50e+03 pdb=" NE2 GLN A 417 " 0.003 2.00e-02 2.50e+03 pdb="HE21 GLN A 417 " 0.307 2.00e-02 2.50e+03 pdb="HE22 GLN A 417 " -0.317 2.00e-02 2.50e+03 ... (remaining 2796 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 1913 2.25 - 2.84: 42325 2.84 - 3.42: 48394 3.42 - 4.01: 65874 4.01 - 4.60: 102270 Nonbonded interactions: 260776 Sorted by model distance: nonbonded pdb=" HE2 HIS A 178 " pdb=" OG1 THR A 362 " model vdw 1.661 1.850 nonbonded pdb=" O ALA A 412 " pdb=" H SER A 415 " model vdw 1.686 1.850 nonbonded pdb=" O THR B 55 " pdb=" H GLY B 60 " model vdw 1.697 1.850 nonbonded pdb="HH21 ARG A 135 " pdb=" OE2 GLU A1019 " model vdw 1.699 1.850 nonbonded pdb=" O THR B 40 " pdb=" HE ARG B 163 " model vdw 1.713 1.850 ... (remaining 260771 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=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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.290 Extract box with map and model: 6.440 Check model and map are aligned: 0.290 Set scattering table: 0.200 Process input model: 66.340 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 : 0.011 0.141 10071 Z= 0.731 Angle : 1.450 16.299 13740 Z= 0.613 Chirality : 0.075 0.514 1582 Planarity : 0.006 0.081 1670 Dihedral : 13.224 179.859 4376 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 0.10 % Allowed : 3.80 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % Twisted General : 0.09 % 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: -3.98 (0.21), residues: 1170 helix: -2.64 (0.16), residues: 609 sheet: -2.58 (0.55), residues: 70 loop : -2.46 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 399 HIS 0.014 0.002 HIS A1099 PHE 0.032 0.003 PHE A 848 TYR 0.026 0.003 TYR B 44 ARG 0.010 0.001 ARG A 602 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 1.614 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 82 LYS cc_start: 0.7071 (tmmt) cc_final: 0.6706 (mmmt) REVERT: A 156 GLN cc_start: 0.7054 (mp10) cc_final: 0.6356 (mp10) REVERT: A 293 ASP cc_start: 0.8244 (m-30) cc_final: 0.8015 (t0) REVERT: A 380 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7805 (tm-30) REVERT: A 460 TRP cc_start: 0.6848 (t-100) cc_final: 0.6592 (t60) REVERT: A 874 LYS cc_start: 0.9235 (ptmm) cc_final: 0.8861 (pttt) REVERT: A 1079 SER cc_start: 0.8939 (p) cc_final: 0.8493 (t) REVERT: B 72 ARG cc_start: 0.7637 (mtp-110) cc_final: 0.7270 (mtm-85) REVERT: B 100 GLN cc_start: 0.7546 (tp40) cc_final: 0.6769 (tp-100) REVERT: B 104 ASP cc_start: 0.7447 (m-30) cc_final: 0.7166 (m-30) outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.6375 time to fit residues: 190.3260 Evaluate side-chains 123 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.0470 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 91 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS A 872 ASN A 889 GLN A 929 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10071 Z= 0.181 Angle : 0.647 7.044 13740 Z= 0.326 Chirality : 0.040 0.179 1582 Planarity : 0.005 0.067 1670 Dihedral : 11.075 178.658 2205 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.70 % Allowed : 9.30 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: -1.96 (0.24), residues: 1170 helix: -0.74 (0.19), residues: 619 sheet: -2.02 (0.60), residues: 67 loop : -1.82 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 844 HIS 0.007 0.001 HIS A 408 PHE 0.020 0.002 PHE A 790 TYR 0.011 0.001 TYR A 373 ARG 0.004 0.001 ARG A1150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 143 time to evaluate : 1.485 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 82 LYS cc_start: 0.7054 (tmmt) cc_final: 0.6657 (mmmt) REVERT: A 101 PHE cc_start: 0.7735 (t80) cc_final: 0.7504 (t80) REVERT: A 293 ASP cc_start: 0.8219 (m-30) cc_final: 0.8001 (t0) REVERT: A 303 ASP cc_start: 0.8051 (t0) cc_final: 0.7843 (t0) REVERT: A 380 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7930 (tm-30) REVERT: A 386 ASN cc_start: 0.8067 (t0) cc_final: 0.7724 (t0) REVERT: A 388 ASN cc_start: 0.8055 (m-40) cc_final: 0.7653 (m-40) REVERT: A 460 TRP cc_start: 0.6799 (t-100) cc_final: 0.6561 (t60) REVERT: A 869 MET cc_start: 0.8067 (tmm) cc_final: 0.7750 (pmm) REVERT: A 874 LYS cc_start: 0.9212 (ptmm) cc_final: 0.8865 (pttt) REVERT: A 901 GLN cc_start: 0.7929 (tt0) cc_final: 0.7602 (tt0) REVERT: A 1079 SER cc_start: 0.8870 (p) cc_final: 0.8510 (t) REVERT: B 100 GLN cc_start: 0.7447 (tp40) cc_final: 0.7210 (tp-100) outliers start: 7 outliers final: 5 residues processed: 150 average time/residue: 0.4610 time to fit residues: 99.8558 Evaluate side-chains 122 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 981 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10071 Z= 0.309 Angle : 0.647 6.100 13740 Z= 0.334 Chirality : 0.042 0.185 1582 Planarity : 0.005 0.068 1670 Dihedral : 9.901 177.916 2205 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 1.80 % Allowed : 10.80 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: -1.21 (0.25), residues: 1170 helix: 0.01 (0.21), residues: 621 sheet: -1.95 (0.58), residues: 78 loop : -1.61 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 278 HIS 0.006 0.001 HIS A 289 PHE 0.023 0.002 PHE A 848 TYR 0.021 0.002 TYR A 193 ARG 0.004 0.001 ARG A 849 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 GLN cc_start: 0.8030 (mp-120) cc_final: 0.7828 (mp10) REVERT: A 374 GLU cc_start: 0.8365 (mp0) cc_final: 0.7723 (mp0) REVERT: A 380 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7969 (tm-30) REVERT: A 388 ASN cc_start: 0.8257 (m-40) cc_final: 0.8030 (m-40) REVERT: A 460 TRP cc_start: 0.6882 (t-100) cc_final: 0.6624 (t60) REVERT: A 597 SER cc_start: 0.8652 (OUTLIER) cc_final: 0.8415 (p) REVERT: A 1079 SER cc_start: 0.9118 (p) cc_final: 0.8667 (t) REVERT: B 100 GLN cc_start: 0.7631 (tp40) cc_final: 0.7203 (tm-30) REVERT: B 104 ASP cc_start: 0.7486 (m-30) cc_final: 0.6745 (m-30) outliers start: 18 outliers final: 12 residues processed: 132 average time/residue: 0.5356 time to fit residues: 100.0101 Evaluate side-chains 120 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 62 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10071 Z= 0.261 Angle : 0.597 5.871 13740 Z= 0.308 Chirality : 0.040 0.167 1582 Planarity : 0.005 0.065 1670 Dihedral : 9.560 179.013 2205 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.20 % Allowed : 12.20 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: -0.75 (0.25), residues: 1170 helix: 0.43 (0.21), residues: 625 sheet: -1.64 (0.60), residues: 77 loop : -1.52 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 844 HIS 0.005 0.001 HIS A 520 PHE 0.016 0.001 PHE A 790 TYR 0.012 0.001 TYR A 193 ARG 0.004 0.000 ARG A1114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7997 (tm-30) REVERT: A 388 ASN cc_start: 0.8279 (m-40) cc_final: 0.8047 (m-40) REVERT: A 460 TRP cc_start: 0.6907 (t-100) cc_final: 0.6626 (t60) REVERT: A 527 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7822 (mm110) REVERT: A 1026 HIS cc_start: 0.7359 (m-70) cc_final: 0.6684 (t70) REVERT: A 1079 SER cc_start: 0.9076 (p) cc_final: 0.8705 (t) REVERT: B 100 GLN cc_start: 0.7736 (tp40) cc_final: 0.6940 (tp-100) REVERT: B 104 ASP cc_start: 0.8014 (m-30) cc_final: 0.7547 (m-30) outliers start: 22 outliers final: 14 residues processed: 133 average time/residue: 0.5051 time to fit residues: 95.3130 Evaluate side-chains 119 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 62 TYR Chi-restraints excluded: chain B residue 70 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10071 Z= 0.171 Angle : 0.555 5.755 13740 Z= 0.284 Chirality : 0.038 0.160 1582 Planarity : 0.004 0.063 1670 Dihedral : 9.115 179.454 2205 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.30 % Allowed : 12.80 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: -0.33 (0.26), residues: 1170 helix: 0.80 (0.22), residues: 622 sheet: -1.14 (0.66), residues: 67 loop : -1.41 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 337 HIS 0.004 0.001 HIS A 289 PHE 0.015 0.001 PHE A 790 TYR 0.011 0.001 TYR A 977 ARG 0.008 0.000 ARG B 153 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 1.537 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 380 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7955 (tm-30) REVERT: A 388 ASN cc_start: 0.8251 (m-40) cc_final: 0.8042 (m-40) REVERT: A 460 TRP cc_start: 0.6791 (t-100) cc_final: 0.6548 (t60) REVERT: A 527 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7826 (mm110) REVERT: A 1079 SER cc_start: 0.9088 (p) cc_final: 0.8742 (t) outliers start: 13 outliers final: 11 residues processed: 125 average time/residue: 0.4380 time to fit residues: 80.5220 Evaluate side-chains 116 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 62 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10071 Z= 0.229 Angle : 0.562 5.785 13740 Z= 0.289 Chirality : 0.039 0.162 1582 Planarity : 0.004 0.061 1670 Dihedral : 8.953 179.788 2205 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.00 % Allowed : 12.90 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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 (0.26), residues: 1170 helix: 0.96 (0.22), residues: 623 sheet: -1.03 (0.67), residues: 67 loop : -1.33 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 844 HIS 0.004 0.001 HIS A 289 PHE 0.015 0.001 PHE A 790 TYR 0.009 0.001 TYR A 977 ARG 0.003 0.000 ARG A1114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8210 (tt) REVERT: A 380 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8028 (tm-30) REVERT: A 388 ASN cc_start: 0.8229 (m-40) cc_final: 0.8003 (m-40) REVERT: A 460 TRP cc_start: 0.6834 (t-100) cc_final: 0.6611 (t60) REVERT: A 1026 HIS cc_start: 0.7421 (m-70) cc_final: 0.6795 (t70) REVERT: A 1079 SER cc_start: 0.9127 (p) cc_final: 0.8741 (t) outliers start: 20 outliers final: 15 residues processed: 121 average time/residue: 0.4352 time to fit residues: 78.7312 Evaluate side-chains 120 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 62 TYR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 85 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.0670 chunk 64 optimal weight: 0.1980 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10071 Z= 0.143 Angle : 0.526 5.627 13740 Z= 0.269 Chirality : 0.037 0.154 1582 Planarity : 0.004 0.057 1670 Dihedral : 8.607 179.780 2205 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.50 % Allowed : 13.50 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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 (0.26), residues: 1170 helix: 1.24 (0.22), residues: 620 sheet: -0.95 (0.67), residues: 67 loop : -1.24 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 337 HIS 0.004 0.001 HIS A1121 PHE 0.015 0.001 PHE A 790 TYR 0.008 0.001 TYR A 977 ARG 0.002 0.000 ARG A1114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 1.671 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 87 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8228 (tt) REVERT: A 380 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7991 (tm-30) REVERT: A 449 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7197 (ttp) REVERT: A 460 TRP cc_start: 0.6806 (t-100) cc_final: 0.6575 (t60) REVERT: A 1026 HIS cc_start: 0.7394 (m-70) cc_final: 0.6815 (t70) REVERT: A 1063 MET cc_start: 0.8432 (ttm) cc_final: 0.8066 (ttm) REVERT: A 1079 SER cc_start: 0.9051 (p) cc_final: 0.8710 (t) outliers start: 15 outliers final: 12 residues processed: 122 average time/residue: 0.4706 time to fit residues: 85.1828 Evaluate side-chains 117 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain B residue 62 TYR Chi-restraints excluded: chain B residue 70 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10071 Z= 0.287 Angle : 0.577 5.721 13740 Z= 0.299 Chirality : 0.040 0.162 1582 Planarity : 0.004 0.059 1670 Dihedral : 8.659 178.980 2205 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.10 % Allowed : 13.80 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: 0.17 (0.26), residues: 1170 helix: 1.23 (0.22), residues: 619 sheet: -0.98 (0.67), residues: 67 loop : -1.20 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 844 HIS 0.005 0.001 HIS A 289 PHE 0.015 0.001 PHE A 848 TYR 0.010 0.001 TYR A 403 ARG 0.004 0.000 ARG A1114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8259 (tt) REVERT: A 380 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8068 (tm-30) REVERT: A 449 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7282 (ttp) REVERT: A 460 TRP cc_start: 0.6851 (t-100) cc_final: 0.6620 (t60) REVERT: A 1063 MET cc_start: 0.8464 (ttm) cc_final: 0.8097 (ttm) outliers start: 21 outliers final: 16 residues processed: 117 average time/residue: 0.4461 time to fit residues: 76.8762 Evaluate side-chains 117 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain B residue 62 TYR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 173 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10071 Z= 0.279 Angle : 0.591 8.945 13740 Z= 0.303 Chirality : 0.040 0.176 1582 Planarity : 0.004 0.061 1670 Dihedral : 8.659 178.794 2205 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 1.80 % Allowed : 14.20 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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 (0.26), residues: 1170 helix: 1.22 (0.22), residues: 623 sheet: -1.05 (0.67), residues: 67 loop : -1.26 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 278 HIS 0.005 0.001 HIS A 289 PHE 0.016 0.001 PHE A 790 TYR 0.011 0.001 TYR A 446 ARG 0.003 0.000 ARG A1114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 1.408 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 87 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8255 (tt) REVERT: A 380 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8074 (tm-30) REVERT: A 460 TRP cc_start: 0.6806 (t-100) cc_final: 0.6587 (t60) REVERT: A 1063 MET cc_start: 0.8510 (ttm) cc_final: 0.8146 (ttm) outliers start: 18 outliers final: 14 residues processed: 112 average time/residue: 0.4229 time to fit residues: 69.4788 Evaluate side-chains 114 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain B residue 62 TYR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 173 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10071 Z= 0.178 Angle : 0.551 7.175 13740 Z= 0.282 Chirality : 0.038 0.178 1582 Planarity : 0.004 0.057 1670 Dihedral : 8.411 178.786 2205 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 1.40 % Allowed : 14.60 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: 0.33 (0.26), residues: 1170 helix: 1.39 (0.22), residues: 623 sheet: -0.98 (0.67), residues: 67 loop : -1.17 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 129 HIS 0.004 0.001 HIS A 289 PHE 0.016 0.001 PHE A 790 TYR 0.009 0.001 TYR A1009 ARG 0.002 0.000 ARG A1114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 1.515 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 87 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8241 (tt) REVERT: A 380 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8065 (tm-30) REVERT: A 460 TRP cc_start: 0.6791 (t-100) cc_final: 0.6584 (t60) REVERT: A 527 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8046 (mm110) REVERT: A 1063 MET cc_start: 0.8483 (ttm) cc_final: 0.8149 (ttm) outliers start: 14 outliers final: 12 residues processed: 109 average time/residue: 0.4522 time to fit residues: 71.6529 Evaluate side-chains 110 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain B residue 62 TYR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 173 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.112681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.090099 restraints weight = 48198.955| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.56 r_work: 0.2996 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10071 Z= 0.195 Angle : 0.554 7.423 13740 Z= 0.284 Chirality : 0.038 0.183 1582 Planarity : 0.004 0.056 1670 Dihedral : 8.293 178.271 2205 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.40 % Allowed : 14.60 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: 0.41 (0.26), residues: 1170 helix: 1.46 (0.22), residues: 624 sheet: -1.01 (0.67), residues: 67 loop : -1.15 (0.31), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 278 HIS 0.004 0.001 HIS A 289 PHE 0.015 0.001 PHE A 790 TYR 0.008 0.001 TYR A1009 ARG 0.003 0.000 ARG A1114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4533.79 seconds wall clock time: 87 minutes 43.07 seconds (5263.07 seconds total)