Starting phenix.real_space_refine on Tue Apr 9 01:44:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t60_41062/04_2024/8t60_41062.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t60_41062/04_2024/8t60_41062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t60_41062/04_2024/8t60_41062.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t60_41062/04_2024/8t60_41062.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t60_41062/04_2024/8t60_41062.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t60_41062/04_2024/8t60_41062.pdb" } resolution = 3.29 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= 1.000 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 126 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 S 34 5.16 5 Na 1 4.78 5 C 4855 2.51 5 N 1216 2.21 5 O 1397 1.98 5 H 7418 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14921 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 417, 6516 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 12, 'TRANS': 404} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Conformer: "B" Number of residues, atoms: 417, 6516 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 12, 'TRANS': 404} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 bond proxies already assigned to first conformer: 6574 Chain: "B" Number of atoms: 1832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1832 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "H" Number of atoms: 3396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 3396 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 11, 'TRANS': 217} Chain: "L" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 3155 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 10, 'TRANS': 199} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.59, per 1000 atoms: 0.71 Number of scatterers: 14921 At special positions: 0 Unit cell: (68.8, 83.42, 173.72, 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) S 34 16.00 Na 1 11.00 O 1397 8.00 N 1216 7.00 C 4855 6.00 H 7418 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.44 Conformation dependent library (CDL) restraints added in 2.2 seconds 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1796 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 14 sheets defined 39.7% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 4 through 36 removed outlier: 3.522A pdb=" N LYS A 8 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A 15 " --> pdb=" O TYR A 11 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILE A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N MET A 30 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N TYR A 31 " --> pdb=" O MET A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 58 removed outlier: 3.895A pdb=" N ASP A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 69 removed outlier: 4.134A pdb=" N MET A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY A 63 " --> pdb=" O ASP A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 95 removed outlier: 3.587A pdb=" N LEU A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.556A pdb=" N PHE A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 134 removed outlier: 4.241A pdb=" N VAL A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Proline residue: A 126 - end of helix removed outlier: 4.745A pdb=" N VAL A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 140 through 145 removed outlier: 3.558A pdb=" N LEU A 144 " --> pdb=" O GLU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 171 removed outlier: 3.769A pdb=" N ARG A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 176 through 200 removed outlier: 3.672A pdb=" N MET A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 Processing helix chain 'A' and resid 230 through 261 removed outlier: 3.563A pdb=" N ALA A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR A 243 " --> pdb=" O MET A 239 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 254 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILE A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N TYR A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 273 Processing helix chain 'A' and resid 274 through 285 removed outlier: 4.058A pdb=" N ALA A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 293 Processing helix chain 'A' and resid 294 through 317 Proline residue: A 306 - end of helix Processing helix chain 'A' and resid 323 through 355 removed outlier: 4.361A pdb=" N VAL A 346 " --> pdb=" O TRP A 342 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 349 " --> pdb=" O GLN A 345 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 395 removed outlier: 3.669A pdb=" N SER A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLN A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR A 373 " --> pdb=" O TYR A 369 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 417 Processing helix chain 'A' and resid 417 through 432 removed outlier: 3.853A pdb=" N PHE A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.697A pdb=" N ASP H 86 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'L' and resid 183 through 187 removed outlier: 3.685A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 183 through 187' Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.572A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 78 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 59 removed outlier: 6.627A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N MET B 34 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.787A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.850A pdb=" N GLY H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 121 through 124 removed outlier: 4.428A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 121 through 124 removed outlier: 4.428A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 151 through 154 removed outlier: 3.995A pdb=" N THR H 205 " --> pdb=" O HIS H 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.407A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.508A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'L' and resid 19 through 23 removed outlier: 3.680A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.605A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 89 through 90 removed outlier: 3.538A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.583A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 153 through 154 385 hydrogen bonds defined for protein. 1076 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: 5.83 Time building geometry restraints manager: 12.76 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: 7414 1.03 - 1.23: 47 1.23 - 1.43: 3272 1.43 - 1.62: 4321 1.62 - 1.82: 54 Bond restraints: 15108 Sorted by residual: bond pdb=" N GLU H 1 " pdb=" CA GLU H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 bond pdb=" N GLU H 1 " pdb=" H GLU H 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C THR A 121 " pdb=" O THR A 121 " ideal model delta sigma weight residual 1.236 1.247 -0.010 1.15e-02 7.56e+03 8.12e-01 bond pdb=" C VAL A 185 " pdb=" O VAL A 185 " ideal model delta sigma weight residual 1.237 1.246 -0.009 1.17e-02 7.31e+03 6.03e-01 bond pdb=" N ILE A 125 " pdb=" CA ILE A 125 " ideal model delta sigma weight residual 1.463 1.472 -0.009 1.20e-02 6.94e+03 5.33e-01 ... (remaining 15103 not shown) Histogram of bond angle deviations from ideal: 100.46 - 107.19: 345 107.19 - 113.92: 17754 113.92 - 120.65: 5122 120.65 - 127.38: 3898 127.38 - 134.11: 90 Bond angle restraints: 27209 Sorted by residual: angle pdb=" N GLY A 395 " pdb=" CA GLY A 395 " pdb=" C GLY A 395 " ideal model delta sigma weight residual 111.12 115.25 -4.13 1.49e+00 4.50e-01 7.67e+00 angle pdb=" N ASP A 124 " pdb=" CA ASP A 124 " pdb=" C ASP A 124 " ideal model delta sigma weight residual 111.69 114.17 -2.48 1.23e+00 6.61e-01 4.08e+00 angle pdb=" CA GLY B 107 " pdb=" C GLY B 107 " pdb=" N LYS B 108 " ideal model delta sigma weight residual 114.61 117.12 -2.51 1.26e+00 6.30e-01 3.98e+00 angle pdb=" N ARG A 139 " pdb=" CA ARG A 139 " pdb=" CB ARG A 139 " ideal model delta sigma weight residual 113.65 110.82 2.83 1.47e+00 4.63e-01 3.71e+00 angle pdb=" N ALA A 173 " pdb=" CA ALA A 173 " pdb=" CB ALA A 173 " ideal model delta sigma weight residual 113.65 110.95 2.70 1.47e+00 4.63e-01 3.38e+00 ... (remaining 27204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 6656 16.61 - 33.23: 373 33.23 - 49.84: 123 49.84 - 66.45: 63 66.45 - 83.06: 4 Dihedral angle restraints: 7219 sinusoidal: 3778 harmonic: 3441 Sorted by residual: dihedral pdb=" CA LEU A 130 " pdb=" C LEU A 130 " pdb=" N VAL A 131 " pdb=" CA VAL A 131 " ideal model delta harmonic sigma weight residual -180.00 -162.94 -17.06 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA LEU A 393 " pdb=" C LEU A 393 " pdb=" N ILE A 394 " pdb=" CA ILE A 394 " ideal model delta harmonic sigma weight residual 180.00 -163.39 -16.61 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA VAL H 142 " pdb=" C VAL H 142 " pdb=" N LYS H 143 " pdb=" CA LYS H 143 " ideal model delta harmonic sigma weight residual -180.00 -164.01 -15.99 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 7216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 776 0.031 - 0.061: 285 0.061 - 0.092: 73 0.092 - 0.123: 59 0.123 - 0.153: 6 Chirality restraints: 1199 Sorted by residual: chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA VAL A 204 " pdb=" N VAL A 204 " pdb=" C VAL A 204 " pdb=" CB VAL A 204 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.50e-01 ... (remaining 1196 not shown) Planarity restraints: 2238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 164 " 0.015 5.00e-02 4.00e+02 2.31e-02 8.53e-01 pdb=" N PRO A 165 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 125 " 0.015 5.00e-02 4.00e+02 2.25e-02 8.07e-01 pdb=" N PRO H 126 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO H 126 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO H 126 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 49 " -0.009 2.00e-02 2.50e+03 5.16e-03 8.00e-01 pdb=" CG TYR L 49 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR L 49 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR L 49 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR L 49 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR L 49 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR L 49 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR L 49 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR L 49 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR L 49 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 TYR L 49 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR L 49 " -0.001 2.00e-02 2.50e+03 ... (remaining 2235 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 1835 2.26 - 2.84: 33084 2.84 - 3.43: 36041 3.43 - 4.01: 49785 4.01 - 4.60: 76207 Nonbonded interactions: 196952 Sorted by model distance: nonbonded pdb=" HH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 1.673 1.850 nonbonded pdb=" O THR A 159 " pdb=" HG1 THR A 163 " model vdw 1.693 1.850 nonbonded pdb=" OD2 ASP L 151 " pdb=" HD1 HIS L 189 " model vdw 1.708 1.850 nonbonded pdb=" OH TYR A 32 " pdb=" HD1 HIS A 98 " model vdw 1.720 1.850 nonbonded pdb=" O ASP L 82 " pdb=" HH TYR L 86 " model vdw 1.722 1.850 ... (remaining 196947 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=0.48 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: 2.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.230 Extract box with map and model: 12.610 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 55.280 Find NCS groups from input model: 0.290 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 : 0.003 0.034 7690 Z= 0.187 Angle : 0.510 4.922 10474 Z= 0.282 Chirality : 0.040 0.153 1199 Planarity : 0.003 0.024 1303 Dihedral : 11.070 81.545 2655 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.85 % Allowed : 8.14 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.28), residues: 967 helix: 2.23 (0.29), residues: 340 sheet: 0.60 (0.37), residues: 224 loop : -1.66 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 106 HIS 0.003 0.001 HIS A 322 PHE 0.012 0.001 PHE A 20 TYR 0.015 0.001 TYR L 49 ARG 0.002 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 293 is missing expected H atoms. Skipping. Residue TYR 355 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue TYR 396 is missing expected H atoms. Skipping. Residue MET 410 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 0.955 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: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8155 (tpt) cc_final: 0.7785 (tpt) REVERT: A 348 MET cc_start: 0.5442 (ttt) cc_final: 0.5209 (tpt) REVERT: A 423 MET cc_start: 0.7815 (ttt) cc_final: 0.7563 (ttm) REVERT: B 4 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8239 (mp) REVERT: B 25 SER cc_start: 0.8167 (p) cc_final: 0.7942 (m) REVERT: B 34 MET cc_start: 0.7314 (mpp) cc_final: 0.6963 (mtt) REVERT: L 170 ASP cc_start: 0.8551 (m-30) cc_final: 0.7813 (p0) outliers start: 15 outliers final: 5 residues processed: 151 average time/residue: 0.4270 time to fit residues: 86.3930 Evaluate side-chains 114 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain H residue 50 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 0.2980 chunk 29 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7818 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7690 Z= 0.166 Angle : 0.524 5.167 10474 Z= 0.279 Chirality : 0.040 0.158 1199 Planarity : 0.003 0.060 1303 Dihedral : 5.179 57.109 1069 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.11 % Allowed : 12.70 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.28), residues: 967 helix: 2.10 (0.28), residues: 341 sheet: 0.61 (0.36), residues: 231 loop : -1.62 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 106 HIS 0.005 0.001 HIS A 322 PHE 0.026 0.001 PHE A 20 TYR 0.022 0.001 TYR A 257 ARG 0.007 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 293 is missing expected H atoms. Skipping. Residue TYR 355 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue TYR 396 is missing expected H atoms. Skipping. Residue MET 410 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 1.027 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 62 MET cc_start: 0.8293 (tpt) cc_final: 0.7973 (tpt) REVERT: A 423 MET cc_start: 0.7763 (ttt) cc_final: 0.7504 (ttm) REVERT: B 4 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8246 (mp) REVERT: B 34 MET cc_start: 0.7324 (mpp) cc_final: 0.6964 (mtt) REVERT: H 79 TYR cc_start: 0.7930 (m-80) cc_final: 0.7722 (m-80) REVERT: L 70 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7530 (m-30) REVERT: L 170 ASP cc_start: 0.8542 (m-30) cc_final: 0.7805 (p0) outliers start: 9 outliers final: 5 residues processed: 123 average time/residue: 0.3785 time to fit residues: 64.8651 Evaluate side-chains 114 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 7690 Z= 0.339 Angle : 0.615 5.977 10474 Z= 0.334 Chirality : 0.042 0.164 1199 Planarity : 0.004 0.043 1303 Dihedral : 5.201 40.989 1065 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 2.34 % Allowed : 14.43 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.27), residues: 967 helix: 1.66 (0.27), residues: 335 sheet: 0.62 (0.35), residues: 242 loop : -1.91 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 106 HIS 0.006 0.001 HIS A 322 PHE 0.019 0.002 PHE A 20 TYR 0.027 0.002 TYR A 257 ARG 0.004 0.001 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 293 is missing expected H atoms. Skipping. Residue TYR 355 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue TYR 396 is missing expected H atoms. Skipping. Residue MET 410 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8341 (tpt) cc_final: 0.7932 (tpt) REVERT: A 423 MET cc_start: 0.7789 (ttt) cc_final: 0.7521 (ttm) REVERT: B 4 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8326 (mp) REVERT: B 34 MET cc_start: 0.7384 (mpp) cc_final: 0.7026 (mtt) REVERT: B 75 LYS cc_start: 0.8891 (mmmt) cc_final: 0.8675 (mmpt) REVERT: H 100 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8541 (mt) REVERT: L 70 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7525 (m-30) REVERT: L 170 ASP cc_start: 0.8649 (m-30) cc_final: 0.7948 (p0) outliers start: 19 outliers final: 7 residues processed: 122 average time/residue: 0.3627 time to fit residues: 63.1781 Evaluate side-chains 109 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 152 ASN Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.0050 chunk 65 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- 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: 0.7875 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7690 Z= 0.193 Angle : 0.538 5.133 10474 Z= 0.289 Chirality : 0.040 0.160 1199 Planarity : 0.003 0.032 1303 Dihedral : 5.009 40.427 1065 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.73 % Allowed : 14.55 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.28), residues: 967 helix: 1.85 (0.28), residues: 335 sheet: 0.60 (0.35), residues: 234 loop : -1.75 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS A 322 PHE 0.017 0.001 PHE A 20 TYR 0.019 0.001 TYR A 257 ARG 0.002 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 293 is missing expected H atoms. Skipping. Residue TYR 355 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue TYR 396 is missing expected H atoms. Skipping. Residue MET 410 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8341 (tpt) cc_final: 0.7960 (tpt) REVERT: A 239 MET cc_start: 0.8248 (mtp) cc_final: 0.8009 (mtp) REVERT: A 423 MET cc_start: 0.7770 (ttt) cc_final: 0.7494 (ttm) REVERT: B 4 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8293 (mp) REVERT: B 34 MET cc_start: 0.7322 (mpp) cc_final: 0.6959 (mtt) REVERT: H 100 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8406 (mt) REVERT: L 170 ASP cc_start: 0.8601 (m-30) cc_final: 0.7871 (p0) outliers start: 14 outliers final: 9 residues processed: 118 average time/residue: 0.3378 time to fit residues: 56.9616 Evaluate side-chains 117 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7860 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7690 Z= 0.173 Angle : 0.522 5.342 10474 Z= 0.279 Chirality : 0.040 0.154 1199 Planarity : 0.003 0.029 1303 Dihedral : 4.709 33.505 1063 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.60 % Allowed : 14.55 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.28), residues: 967 helix: 1.96 (0.28), residues: 335 sheet: 0.66 (0.36), residues: 233 loop : -1.64 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS A 322 PHE 0.016 0.001 PHE A 20 TYR 0.018 0.001 TYR A 257 ARG 0.003 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 293 is missing expected H atoms. Skipping. Residue TYR 355 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue TYR 396 is missing expected H atoms. Skipping. Residue MET 410 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8387 (tpt) cc_final: 0.8024 (tpt) REVERT: A 239 MET cc_start: 0.8261 (mtp) cc_final: 0.8011 (mtp) REVERT: A 423 MET cc_start: 0.7751 (ttt) cc_final: 0.7478 (ttm) REVERT: B 4 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8281 (mp) REVERT: B 34 MET cc_start: 0.7356 (mpp) cc_final: 0.6943 (mtt) REVERT: B 75 LYS cc_start: 0.8867 (mmmt) cc_final: 0.8378 (mmtt) REVERT: L 70 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7610 (m-30) REVERT: L 170 ASP cc_start: 0.8616 (m-30) cc_final: 0.7889 (p0) outliers start: 13 outliers final: 9 residues processed: 115 average time/residue: 0.3662 time to fit residues: 60.1448 Evaluate side-chains 114 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 152 ASN Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7690 Z= 0.287 Angle : 0.577 4.983 10474 Z= 0.315 Chirality : 0.041 0.159 1199 Planarity : 0.004 0.030 1303 Dihedral : 4.921 31.081 1061 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.10 % Allowed : 14.80 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.27), residues: 967 helix: 1.61 (0.28), residues: 335 sheet: 0.62 (0.35), residues: 233 loop : -1.83 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 47 HIS 0.004 0.001 HIS A 322 PHE 0.011 0.001 PHE H 146 TYR 0.022 0.002 TYR A 257 ARG 0.003 0.000 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 293 is missing expected H atoms. Skipping. Residue TYR 355 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue TYR 396 is missing expected H atoms. Skipping. Residue MET 410 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8376 (tpt) cc_final: 0.7950 (tpt) REVERT: A 239 MET cc_start: 0.8209 (mtp) cc_final: 0.7989 (mtp) REVERT: A 257 TYR cc_start: 0.8209 (t80) cc_final: 0.7969 (t80) REVERT: A 423 MET cc_start: 0.7786 (ttt) cc_final: 0.7507 (ttm) REVERT: B 4 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8391 (mp) REVERT: B 34 MET cc_start: 0.7480 (mpp) cc_final: 0.7132 (mtt) REVERT: B 75 LYS cc_start: 0.8945 (mmmt) cc_final: 0.8600 (mmtt) REVERT: H 100 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8490 (mt) REVERT: L 70 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7606 (m-30) REVERT: L 170 ASP cc_start: 0.8695 (m-30) cc_final: 0.7987 (p0) outliers start: 17 outliers final: 11 residues processed: 116 average time/residue: 0.3346 time to fit residues: 56.2575 Evaluate side-chains 113 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 152 ASN Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 0.0770 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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: 0.7868 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7690 Z= 0.164 Angle : 0.514 4.788 10474 Z= 0.275 Chirality : 0.040 0.159 1199 Planarity : 0.003 0.030 1303 Dihedral : 4.655 31.695 1061 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.73 % Allowed : 15.41 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.28), residues: 967 helix: 1.87 (0.28), residues: 336 sheet: 0.93 (0.37), residues: 210 loop : -1.69 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS A 322 PHE 0.013 0.001 PHE A 20 TYR 0.015 0.001 TYR A 257 ARG 0.002 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 293 is missing expected H atoms. Skipping. Residue TYR 355 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue TYR 396 is missing expected H atoms. Skipping. Residue MET 410 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8355 (tpt) cc_final: 0.7986 (tpt) REVERT: A 239 MET cc_start: 0.8205 (mtp) cc_final: 0.7965 (mtp) REVERT: A 423 MET cc_start: 0.7751 (ttt) cc_final: 0.7475 (ttm) REVERT: B 4 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8320 (mp) REVERT: B 34 MET cc_start: 0.7396 (mpp) cc_final: 0.7035 (mtt) REVERT: B 75 LYS cc_start: 0.8901 (mmmt) cc_final: 0.8592 (mmtt) REVERT: H 100 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8378 (mt) REVERT: L 170 ASP cc_start: 0.8646 (m-30) cc_final: 0.7882 (p0) outliers start: 14 outliers final: 10 residues processed: 114 average time/residue: 0.3675 time to fit residues: 60.9450 Evaluate side-chains 113 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 80 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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: 0.7846 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7690 Z= 0.157 Angle : 0.505 6.644 10474 Z= 0.268 Chirality : 0.040 0.153 1199 Planarity : 0.003 0.029 1303 Dihedral : 4.482 32.251 1061 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.36 % Allowed : 15.78 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.28), residues: 967 helix: 2.02 (0.28), residues: 337 sheet: 0.92 (0.36), residues: 218 loop : -1.58 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS A 322 PHE 0.013 0.001 PHE A 20 TYR 0.025 0.001 TYR A 257 ARG 0.002 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 293 is missing expected H atoms. Skipping. Residue TYR 355 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue TYR 396 is missing expected H atoms. Skipping. Residue MET 410 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8383 (tpt) cc_final: 0.8097 (tpt) REVERT: A 239 MET cc_start: 0.8238 (mtp) cc_final: 0.8005 (mtp) REVERT: B 4 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8243 (mp) REVERT: B 34 MET cc_start: 0.7409 (mpp) cc_final: 0.7027 (mtt) REVERT: B 75 LYS cc_start: 0.8895 (mmmt) cc_final: 0.8608 (mmtt) REVERT: H 100 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8290 (mt) REVERT: L 170 ASP cc_start: 0.8635 (m-30) cc_final: 0.7865 (p0) outliers start: 11 outliers final: 8 residues processed: 110 average time/residue: 0.3530 time to fit residues: 55.2506 Evaluate side-chains 110 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 51 optimal weight: 0.1980 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 0.0060 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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: 0.7821 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7690 Z= 0.144 Angle : 0.489 5.060 10474 Z= 0.258 Chirality : 0.039 0.147 1199 Planarity : 0.003 0.030 1303 Dihedral : 4.352 32.986 1061 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.60 % Allowed : 15.66 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.28), residues: 967 helix: 2.15 (0.28), residues: 337 sheet: 0.93 (0.36), residues: 220 loop : -1.52 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.004 0.001 HIS A 322 PHE 0.012 0.001 PHE A 20 TYR 0.019 0.001 TYR A 257 ARG 0.002 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 293 is missing expected H atoms. Skipping. Residue TYR 355 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue TYR 396 is missing expected H atoms. Skipping. Residue MET 410 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 1.038 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 239 MET cc_start: 0.8209 (mtp) cc_final: 0.7994 (mtp) REVERT: B 4 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8229 (mp) REVERT: B 34 MET cc_start: 0.7414 (mpp) cc_final: 0.7027 (mtt) REVERT: B 75 LYS cc_start: 0.8901 (mmmt) cc_final: 0.8634 (mmtt) REVERT: H 100 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8293 (mt) REVERT: L 170 ASP cc_start: 0.8636 (m-30) cc_final: 0.7854 (p0) outliers start: 13 outliers final: 9 residues processed: 115 average time/residue: 0.3788 time to fit residues: 61.3544 Evaluate side-chains 116 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 0.3980 chunk 60 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 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: 0.7834 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7690 Z= 0.162 Angle : 0.498 6.018 10474 Z= 0.264 Chirality : 0.039 0.146 1199 Planarity : 0.003 0.030 1303 Dihedral : 4.344 32.826 1061 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.73 % Allowed : 15.78 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.28), residues: 967 helix: 2.14 (0.28), residues: 337 sheet: 0.94 (0.36), residues: 220 loop : -1.52 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.005 0.001 HIS A 322 PHE 0.013 0.001 PHE B 121 TYR 0.028 0.001 TYR A 257 ARG 0.002 0.000 ARG A 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 293 is missing expected H atoms. Skipping. Residue TYR 355 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue TYR 396 is missing expected H atoms. Skipping. Residue MET 410 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 1.172 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 239 MET cc_start: 0.8169 (mtp) cc_final: 0.7967 (mtp) REVERT: B 4 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8238 (mp) REVERT: B 34 MET cc_start: 0.7447 (mpp) cc_final: 0.7071 (mtt) REVERT: B 75 LYS cc_start: 0.8883 (mmmt) cc_final: 0.8637 (mmtt) REVERT: H 100 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8300 (mt) REVERT: L 11 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8246 (mp) REVERT: L 170 ASP cc_start: 0.8650 (m-30) cc_final: 0.7868 (p0) outliers start: 14 outliers final: 10 residues processed: 116 average time/residue: 0.3733 time to fit residues: 60.7461 Evaluate side-chains 115 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.135789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.113635 restraints weight = 45919.279| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.86 r_work: 0.3609 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7690 Z= 0.183 Angle : 0.509 5.885 10474 Z= 0.271 Chirality : 0.040 0.148 1199 Planarity : 0.003 0.029 1303 Dihedral : 4.421 32.411 1061 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.60 % Allowed : 16.03 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.28), residues: 967 helix: 2.10 (0.28), residues: 337 sheet: 0.96 (0.36), residues: 218 loop : -1.52 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.005 0.001 HIS A 322 PHE 0.010 0.001 PHE A 20 TYR 0.022 0.001 TYR A 257 ARG 0.002 0.000 ARG A 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4027.18 seconds wall clock time: 72 minutes 23.21 seconds (4343.21 seconds total)