Starting phenix.real_space_refine on Wed Sep 25 03:10:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq0_25373/09_2024/7sq0_25373.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq0_25373/09_2024/7sq0_25373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq0_25373/09_2024/7sq0_25373.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq0_25373/09_2024/7sq0_25373.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq0_25373/09_2024/7sq0_25373.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq0_25373/09_2024/7sq0_25373.cif" } resolution = 3.7 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= 0.001 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 54 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: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4 5.49 5 Mg 2 5.21 5 S 32 5.16 5 C 3089 2.51 5 N 814 2.21 5 O 932 1.98 5 H 4286 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9160 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1421 Classifications: {'peptide': 94} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 88} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 3059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3059 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 9, 'TRANS': 202} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1429 Classifications: {'peptide': 94} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "B" Number of atoms: 3056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3056 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 138 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3490 SG CYS A 287 30.096 41.595 78.100 1.00 78.54 S ATOM 3529 SG CYS A 290 30.245 44.327 76.040 1.00 79.84 S ATOM 7977 SG CYS B 287 27.060 45.006 78.102 1.00 78.23 S ATOM 8016 SG CYS B 290 26.901 42.269 76.059 1.00 79.43 S Time building chain proxies: 5.28, per 1000 atoms: 0.58 Number of scatterers: 9160 At special positions: 0 Unit cell: (58.022, 87.466, 91.796, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 32 16.00 P 4 15.00 Mg 2 11.99 O 932 8.00 N 814 7.00 C 3089 6.00 H 4286 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.77 Conformation dependent library (CDL) restraints added in 620.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 500 " pdb="ZN ZN A 500 " - pdb=" SG CYS B 290 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 290 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 287 " pdb="ZN ZN A 500 " - pdb=" SG CYS B 287 " Number of angles added : 6 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1210 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 2 sheets defined 62.2% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 5 through 11 removed outlier: 3.829A pdb=" N LEU A 9 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP A 10 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN A 11 " --> pdb=" O ASP A 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 5 through 11' Processing helix chain 'A' and resid 26 through 42 Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.706A pdb=" N MET A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 116 removed outlier: 3.614A pdb=" N UNK A 105 " --> pdb=" O UNK A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 135 removed outlier: 4.093A pdb=" N GLY A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 155 removed outlier: 3.806A pdb=" N THR A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 189 removed outlier: 3.564A pdb=" N LEU A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ARG A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.515A pdb=" N GLU A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 236 removed outlier: 3.516A pdb=" N ASP A 225 " --> pdb=" O TYR A 221 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 removed outlier: 4.362A pdb=" N TYR A 254 " --> pdb=" O PHE A 250 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 266 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 308 removed outlier: 3.719A pdb=" N LYS A 299 " --> pdb=" O ARG A 295 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR A 300 " --> pdb=" O MET A 296 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.871A pdb=" N ASP A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU A 334 " --> pdb=" O ARG A 330 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 removed outlier: 3.827A pdb=" N LEU B 9 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 10 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN B 11 " --> pdb=" O ASP B 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 5 through 11' Processing helix chain 'B' and resid 26 through 42 Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 88 through 94 Processing helix chain 'B' and resid 98 through 114 removed outlier: 3.659A pdb=" N UNK B 102 " --> pdb=" O UNK B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 135 removed outlier: 3.723A pdb=" N PHE B 131 " --> pdb=" O CYS B 127 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP B 134 " --> pdb=" O SER B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 155 removed outlier: 3.823A pdb=" N THR B 155 " --> pdb=" O LYS B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 189 removed outlier: 3.537A pdb=" N LEU B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG B 173 " --> pdb=" O GLY B 169 " (cutoff:3.500A) Proline residue: B 178 - end of helix removed outlier: 3.581A pdb=" N LYS B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 236 removed outlier: 3.570A pdb=" N ARG B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 removed outlier: 4.369A pdb=" N TYR B 254 " --> pdb=" O PHE B 250 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 308 removed outlier: 3.724A pdb=" N LYS B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR B 300 " --> pdb=" O MET B 296 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 338 removed outlier: 3.869A pdb=" N ASP B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B 334 " --> pdb=" O ARG B 330 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR B 335 " --> pdb=" O ASP B 331 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU B 336 " --> pdb=" O TYR B 332 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 281 removed outlier: 3.562A pdb=" N TYR C 280 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR C 281 " --> pdb=" O ILE C 277 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 72 removed outlier: 6.945A pdb=" N LEU A 48 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ASP A 164 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU A 50 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE A 19 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N PHE A 242 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N VAL A 274 " --> pdb=" O PHE A 242 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLY A 244 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ASN A 276 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N CYS A 246 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL A 278 " --> pdb=" O CYS A 246 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 277 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 71 through 72 removed outlier: 6.934A pdb=" N LEU B 48 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N ASP B 164 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU B 50 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 19 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N ALA B 272 " --> pdb=" O CYS B 240 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N PHE B 242 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N VAL B 274 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLY B 244 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ASN B 276 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS B 246 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL B 278 " --> pdb=" O CYS B 246 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE B 277 " --> pdb=" O SER B 316 " (cutoff:3.500A) 243 hydrogen bonds defined for protein. 723 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: 2.96 Time building geometry restraints manager: 3.20 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: 4274 1.03 - 1.23: 12 1.23 - 1.42: 2072 1.42 - 1.61: 2850 1.61 - 1.81: 50 Bond restraints: 9258 Sorted by residual: bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C5 ADP B 401 " pdb=" C6 ADP B 401 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C5 ADP A 401 " pdb=" C6 ADP A 401 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C8 ADP B 401 " pdb=" N7 ADP B 401 " ideal model delta sigma weight residual 1.350 1.309 0.041 2.00e-02 2.50e+03 4.17e+00 ... (remaining 9253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.88: 16484 7.88 - 15.76: 10 15.76 - 23.64: 2 23.64 - 31.52: 4 31.52 - 39.40: 9 Bond angle restraints: 16509 Sorted by residual: angle pdb=" C PRO A 222 " pdb=" CA PRO A 222 " pdb=" HA PRO A 222 " ideal model delta sigma weight residual 109.00 69.60 39.40 3.00e+00 1.11e-01 1.73e+02 angle pdb=" CB LEU C 272 " pdb=" CA LEU C 272 " pdb=" HA LEU C 272 " ideal model delta sigma weight residual 109.00 73.92 35.08 3.00e+00 1.11e-01 1.37e+02 angle pdb=" CB LYS A 223 " pdb=" CA LYS A 223 " pdb=" HA LYS A 223 " ideal model delta sigma weight residual 109.00 74.23 34.77 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C LYS A 223 " pdb=" CA LYS A 223 " pdb=" HA LYS A 223 " ideal model delta sigma weight residual 109.00 74.47 34.53 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C LEU C 272 " pdb=" CA LEU C 272 " pdb=" HA LEU C 272 " ideal model delta sigma weight residual 109.00 74.77 34.23 3.00e+00 1.11e-01 1.30e+02 ... (remaining 16504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.01: 4343 28.01 - 56.02: 77 56.02 - 84.03: 20 84.03 - 112.03: 0 112.03 - 140.04: 6 Dihedral angle restraints: 4446 sinusoidal: 2288 harmonic: 2158 Sorted by residual: dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 159.96 140.04 1 2.00e+01 2.50e-03 4.24e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 160.15 139.85 1 2.00e+01 2.50e-03 4.23e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 179.63 120.37 1 2.00e+01 2.50e-03 3.61e+01 ... (remaining 4443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 732 0.084 - 0.168: 45 0.168 - 0.252: 0 0.252 - 0.336: 2 0.336 - 0.420: 3 Chirality restraints: 782 Sorted by residual: chirality pdb=" CA PRO A 222 " pdb=" N PRO A 222 " pdb=" C PRO A 222 " pdb=" CB PRO A 222 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CA LEU C 272 " pdb=" N LEU C 272 " pdb=" C LEU C 272 " pdb=" CB LEU C 272 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA LYS A 223 " pdb=" N LYS A 223 " pdb=" C LYS A 223 " pdb=" CB LYS A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 779 not shown) Planarity restraints: 1384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 285 " 0.010 5.00e-02 4.00e+02 1.46e-02 3.40e-01 pdb=" N PRO A 286 " -0.025 5.00e-02 4.00e+02 pdb=" CA PRO A 286 " 0.007 5.00e-02 4.00e+02 pdb=" CD PRO A 286 " 0.008 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 285 " 0.009 5.00e-02 4.00e+02 1.44e-02 3.30e-01 pdb=" N PRO B 286 " -0.025 5.00e-02 4.00e+02 pdb=" CA PRO B 286 " 0.007 5.00e-02 4.00e+02 pdb=" CD PRO B 286 " 0.008 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 247 " 0.009 5.00e-02 4.00e+02 1.39e-02 3.07e-01 pdb=" N PRO A 248 " -0.024 5.00e-02 4.00e+02 pdb=" CA PRO A 248 " 0.007 5.00e-02 4.00e+02 pdb=" CD PRO A 248 " 0.008 5.00e-02 4.00e+02 ... (remaining 1381 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 630 2.22 - 2.82: 18708 2.82 - 3.41: 21212 3.41 - 4.01: 27821 4.01 - 4.60: 43887 Nonbonded interactions: 112258 Sorted by model distance: nonbonded pdb=" H LYS A 223 " pdb=" HA LYS A 223 " model vdw 1.630 1.816 nonbonded pdb=" O GLY B 26 " pdb=" HG1 THR B 30 " model vdw 1.698 2.450 nonbonded pdb=" O PRO A 43 " pdb="HD21 ASN A 78 " model vdw 1.709 2.450 nonbonded pdb=" O GLN C 262 " pdb=" H LEU C 266 " model vdw 1.710 2.450 nonbonded pdb=" O PRO B 43 " pdb="HD22 ASN B 78 " model vdw 1.712 2.450 ... (remaining 112253 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 94 or resid 99 through 116 or resid 126 through \ 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or re \ sid 133 through 189 or resid 221 through 346 or resid 501)) selection = (chain 'B' and (resid 1 through 88 or (resid 89 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 90 through 94 or resid 97 \ through 136 or (resid 137 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or res \ id 138 through 184 or (resid 185 and (name N or name CA or name C or name O or n \ ame CB or name CG or name CD1 or name CD2 or name H or name HA )) or resid 186 t \ hrough 222 or (resid 223 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name CE or name NZ or name H or name HA )) or resid 224 \ through 345 or (resid 346 and (name N or name CA or name C or name O or name CB \ )) or resid 501)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.170 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.460 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.004 0.108 4972 Z= 0.247 Angle : 0.678 13.259 6761 Z= 0.284 Chirality : 0.045 0.420 782 Planarity : 0.001 0.015 858 Dihedral : 13.617 140.043 1765 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.31), residues: 579 helix: -2.00 (0.26), residues: 273 sheet: -1.96 (0.65), residues: 44 loop : -1.63 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 344 HIS 0.001 0.000 HIS A 56 PHE 0.004 0.001 PHE B 62 TYR 0.005 0.001 TYR A 340 ARG 0.001 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 267 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue ALA 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.697 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 151 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8352 (ttmm) REVERT: A 165 THR cc_start: 0.9253 (p) cc_final: 0.8964 (t) REVERT: A 235 ARG cc_start: 0.8303 (ttm110) cc_final: 0.7540 (mtt90) REVERT: B 151 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8343 (ttmm) REVERT: B 165 THR cc_start: 0.9217 (p) cc_final: 0.8918 (t) REVERT: B 183 LYS cc_start: 0.8292 (tppt) cc_final: 0.8045 (ttpt) REVERT: B 235 ARG cc_start: 0.8219 (ttm110) cc_final: 0.7631 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.3793 time to fit residues: 48.5413 Evaluate side-chains 76 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4972 Z= 0.261 Angle : 0.602 6.433 6761 Z= 0.298 Chirality : 0.048 0.399 782 Planarity : 0.004 0.025 858 Dihedral : 12.479 151.906 687 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.79 % Allowed : 6.31 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.34), residues: 579 helix: -0.08 (0.29), residues: 294 sheet: -1.91 (0.64), residues: 44 loop : -1.16 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 144 HIS 0.003 0.001 HIS B 56 PHE 0.009 0.001 PHE B 174 TYR 0.007 0.001 TYR B 340 ARG 0.002 0.000 ARG B 295 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 267 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue ALA 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 THR cc_start: 0.9387 (p) cc_final: 0.9169 (t) REVERT: B 144 TRP cc_start: 0.7492 (m100) cc_final: 0.7245 (m100) REVERT: B 165 THR cc_start: 0.9403 (p) cc_final: 0.9192 (t) REVERT: B 183 LYS cc_start: 0.8512 (tppt) cc_final: 0.8259 (ttpt) REVERT: B 309 ASP cc_start: 0.8056 (p0) cc_final: 0.7835 (p0) outliers start: 4 outliers final: 3 residues processed: 80 average time/residue: 0.2939 time to fit residues: 31.2355 Evaluate side-chains 68 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain B residue 84 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 15 optimal weight: 0.4980 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4972 Z= 0.150 Angle : 0.539 6.190 6761 Z= 0.253 Chirality : 0.046 0.396 782 Planarity : 0.003 0.029 858 Dihedral : 11.374 137.520 687 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.39 % Allowed : 9.66 % Favored : 89.94 % 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: 0.03 (0.35), residues: 579 helix: 1.06 (0.31), residues: 294 sheet: -1.61 (0.63), residues: 44 loop : -0.91 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 144 HIS 0.001 0.000 HIS B 12 PHE 0.013 0.001 PHE B 146 TYR 0.010 0.001 TYR B 254 ARG 0.001 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 267 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue ALA 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 THR cc_start: 0.9405 (p) cc_final: 0.9185 (t) REVERT: A 338 LYS cc_start: 0.8175 (pttt) cc_final: 0.7905 (mmmm) REVERT: B 165 THR cc_start: 0.9430 (p) cc_final: 0.9228 (t) outliers start: 2 outliers final: 2 residues processed: 76 average time/residue: 0.3012 time to fit residues: 30.3079 Evaluate side-chains 71 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 84 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4972 Z= 0.154 Angle : 0.535 5.849 6761 Z= 0.250 Chirality : 0.046 0.395 782 Planarity : 0.003 0.028 858 Dihedral : 11.295 164.139 687 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.59 % Allowed : 10.45 % Favored : 88.95 % 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: 0.42 (0.36), residues: 579 helix: 1.45 (0.31), residues: 294 sheet: -1.68 (0.62), residues: 48 loop : -0.74 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 144 HIS 0.001 0.001 HIS A 6 PHE 0.005 0.001 PHE A 62 TYR 0.010 0.001 TYR A 254 ARG 0.001 0.000 ARG B 295 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 267 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue ALA 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 THR cc_start: 0.9409 (p) cc_final: 0.9189 (t) REVERT: A 338 LYS cc_start: 0.8155 (pttt) cc_final: 0.7907 (mmmm) REVERT: B 165 THR cc_start: 0.9431 (p) cc_final: 0.9220 (t) outliers start: 3 outliers final: 2 residues processed: 69 average time/residue: 0.2790 time to fit residues: 26.0928 Evaluate side-chains 65 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 84 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4972 Z= 0.305 Angle : 0.599 6.792 6761 Z= 0.290 Chirality : 0.048 0.400 782 Planarity : 0.004 0.035 858 Dihedral : 12.308 177.165 687 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.18 % Allowed : 11.64 % Favored : 87.18 % 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: 0.19 (0.35), residues: 579 helix: 1.20 (0.31), residues: 293 sheet: -1.57 (0.65), residues: 48 loop : -0.81 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 144 HIS 0.003 0.001 HIS A 6 PHE 0.008 0.001 PHE A 277 TYR 0.007 0.001 TYR A 340 ARG 0.001 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 267 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue ALA 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 THR cc_start: 0.9441 (p) cc_final: 0.9228 (t) REVERT: A 338 LYS cc_start: 0.8224 (pttt) cc_final: 0.7982 (mmmm) REVERT: B 165 THR cc_start: 0.9445 (p) cc_final: 0.9233 (t) outliers start: 6 outliers final: 6 residues processed: 68 average time/residue: 0.2728 time to fit residues: 25.1965 Evaluate side-chains 67 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 307 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4972 Z= 0.206 Angle : 0.559 6.100 6761 Z= 0.263 Chirality : 0.047 0.398 782 Planarity : 0.004 0.034 858 Dihedral : 11.881 175.741 687 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.79 % Allowed : 12.82 % Favored : 86.39 % 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: 0.38 (0.35), residues: 579 helix: 1.36 (0.31), residues: 294 sheet: -1.43 (0.66), residues: 48 loop : -0.74 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 144 HIS 0.002 0.001 HIS A 56 PHE 0.006 0.001 PHE B 242 TYR 0.007 0.001 TYR B 254 ARG 0.001 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 267 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue ALA 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TRP cc_start: 0.7792 (m100) cc_final: 0.7466 (m100) REVERT: A 165 THR cc_start: 0.9458 (p) cc_final: 0.9228 (t) REVERT: A 338 LYS cc_start: 0.8194 (pttt) cc_final: 0.7959 (mmmm) REVERT: B 165 THR cc_start: 0.9459 (p) cc_final: 0.9234 (t) outliers start: 4 outliers final: 3 residues processed: 66 average time/residue: 0.2881 time to fit residues: 25.7095 Evaluate side-chains 65 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 140 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 58 optimal weight: 0.0000 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4972 Z= 0.128 Angle : 0.528 6.319 6761 Z= 0.242 Chirality : 0.046 0.397 782 Planarity : 0.003 0.030 858 Dihedral : 10.965 178.323 687 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.20 % Allowed : 13.02 % Favored : 86.79 % 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: 0.77 (0.36), residues: 579 helix: 1.66 (0.31), residues: 294 sheet: -1.13 (0.66), residues: 48 loop : -0.54 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 144 HIS 0.001 0.000 HIS A 56 PHE 0.006 0.001 PHE B 146 TYR 0.007 0.001 TYR B 254 ARG 0.001 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 267 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue ALA 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 THR cc_start: 0.9431 (p) cc_final: 0.9212 (t) REVERT: B 165 THR cc_start: 0.9456 (p) cc_final: 0.9237 (t) REVERT: B 338 LYS cc_start: 0.8202 (pttt) cc_final: 0.7976 (mmmm) outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.3063 time to fit residues: 26.4427 Evaluate side-chains 66 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.0980 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4972 Z= 0.147 Angle : 0.532 6.452 6761 Z= 0.245 Chirality : 0.046 0.398 782 Planarity : 0.003 0.031 858 Dihedral : 10.133 177.137 687 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.20 % Allowed : 13.02 % Favored : 86.79 % 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: 0.96 (0.36), residues: 579 helix: 1.80 (0.31), residues: 294 sheet: -0.90 (0.68), residues: 48 loop : -0.47 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 144 HIS 0.001 0.000 HIS A 56 PHE 0.008 0.001 PHE B 146 TYR 0.006 0.001 TYR B 254 ARG 0.001 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 267 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue ALA 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 THR cc_start: 0.9427 (p) cc_final: 0.9210 (t) REVERT: B 165 THR cc_start: 0.9424 (p) cc_final: 0.9205 (t) REVERT: B 338 LYS cc_start: 0.8190 (pttt) cc_final: 0.7986 (mmmm) outliers start: 1 outliers final: 1 residues processed: 63 average time/residue: 0.2886 time to fit residues: 24.7115 Evaluate side-chains 63 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4972 Z= 0.228 Angle : 0.560 6.209 6761 Z= 0.265 Chirality : 0.047 0.399 782 Planarity : 0.004 0.035 858 Dihedral : 9.524 154.588 687 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.20 % Allowed : 13.61 % 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: 0.79 (0.36), residues: 579 helix: 1.60 (0.31), residues: 300 sheet: -0.94 (0.69), residues: 48 loop : -0.53 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 144 HIS 0.003 0.001 HIS B 6 PHE 0.007 0.001 PHE A 277 TYR 0.006 0.001 TYR B 332 ARG 0.001 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 267 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue ALA 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TRP cc_start: 0.7327 (m-10) cc_final: 0.7095 (m-10) REVERT: A 165 THR cc_start: 0.9416 (p) cc_final: 0.9203 (t) REVERT: B 165 THR cc_start: 0.9424 (p) cc_final: 0.9206 (t) REVERT: B 338 LYS cc_start: 0.8199 (pttt) cc_final: 0.7991 (mmmm) outliers start: 1 outliers final: 1 residues processed: 58 average time/residue: 0.2976 time to fit residues: 23.2800 Evaluate side-chains 60 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4972 Z= 0.144 Angle : 0.529 6.577 6761 Z= 0.244 Chirality : 0.046 0.398 782 Planarity : 0.003 0.033 858 Dihedral : 9.205 155.034 687 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.20 % Allowed : 13.81 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.36), residues: 579 helix: 1.92 (0.31), residues: 300 sheet: -0.79 (0.70), residues: 48 loop : -0.39 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 144 HIS 0.001 0.000 HIS A 56 PHE 0.004 0.001 PHE B 131 TYR 0.006 0.001 TYR B 254 ARG 0.001 0.000 ARG B 235 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 267 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue ALA 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 THR cc_start: 0.9420 (p) cc_final: 0.9205 (t) REVERT: B 165 THR cc_start: 0.9426 (p) cc_final: 0.9203 (t) outliers start: 1 outliers final: 1 residues processed: 61 average time/residue: 0.3284 time to fit residues: 27.2966 Evaluate side-chains 61 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.118053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.089168 restraints weight = 23566.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.093471 restraints weight = 11837.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.096369 restraints weight = 7734.571| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4972 Z= 0.140 Angle : 0.529 5.997 6761 Z= 0.243 Chirality : 0.046 0.398 782 Planarity : 0.003 0.031 858 Dihedral : 8.819 149.386 687 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.20 % Allowed : 13.81 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.37), residues: 579 helix: 2.09 (0.31), residues: 301 sheet: -0.49 (0.71), residues: 48 loop : -0.36 (0.43), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 144 HIS 0.001 0.000 HIS A 56 PHE 0.004 0.001 PHE B 311 TYR 0.006 0.001 TYR B 254 ARG 0.001 0.000 ARG B 235 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2442.15 seconds wall clock time: 43 minutes 8.31 seconds (2588.31 seconds total)