Starting phenix.real_space_refine on Wed Feb 14 06:23:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo9_14844/02_2024/7zo9_14844_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo9_14844/02_2024/7zo9_14844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo9_14844/02_2024/7zo9_14844.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo9_14844/02_2024/7zo9_14844.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo9_14844/02_2024/7zo9_14844_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo9_14844/02_2024/7zo9_14844_neut_updated.pdb" } resolution = 3.5 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= 0.005 sd= 0.090 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 64 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 V 2 8.30 5 P 4 5.49 5 S 44 5.16 5 C 5526 2.51 5 N 1534 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8730 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4333 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 556, 4317 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} Conformer: "B" Number of residues, atoms: 556, 4317 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} bond proxies already assigned to first conformer: 4380 Conformer: "C" Number of residues, atoms: 556, 4317 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} bond proxies already assigned to first conformer: 4380 Chain: "B" Number of atoms: 4333 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 556, 4317 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} Conformer: "B" Number of residues, atoms: 556, 4317 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} bond proxies already assigned to first conformer: 4380 Conformer: "C" Number of residues, atoms: 556, 4317 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} bond proxies already assigned to first conformer: 4380 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.64, per 1000 atoms: 1.45 Number of scatterers: 8730 At special positions: 0 Unit cell: (85.075, 76.875, 131.2, 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) V 2 22.97 S 44 16.00 P 4 15.00 O 1620 8.00 N 1534 7.00 C 5526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.59 Conformation dependent library (CDL) restraints added in 4.4 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 4 sheets defined 63.7% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 18 through 45 removed outlier: 4.026A pdb=" N THR A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 57 through 100 removed outlier: 4.093A pdb=" N MET A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 114 through 153 removed outlier: 3.881A pdb=" N SER A 125 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 156 through 211 removed outlier: 3.845A pdb=" N ARG A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N SER A 206 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 265 removed outlier: 3.660A pdb=" N ALA A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Proline residue: A 234 - end of helix removed outlier: 4.110A pdb=" N VAL A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 315 removed outlier: 4.842A pdb=" N VAL A 275 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE A 292 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA A 294 " --> pdb=" O GLN A 291 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG A 303 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET A 312 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP A 314 " --> pdb=" O GLN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 381 Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 438 through 447 Processing helix chain 'A' and resid 451 through 454 No H-bonds generated for 'chain 'A' and resid 451 through 454' Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 504 through 518 removed outlier: 3.769A pdb=" N ALA A 513 " --> pdb=" O LYS A 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 18 through 45 removed outlier: 4.026A pdb=" N THR B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 57 through 100 removed outlier: 4.093A pdb=" N MET B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 114 through 153 removed outlier: 3.880A pdb=" N SER B 125 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Proline residue: B 149 - end of helix Processing helix chain 'B' and resid 156 through 211 removed outlier: 3.845A pdb=" N ARG B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS B 179 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA B 186 " --> pdb=" O ASP B 182 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN B 204 " --> pdb=" O ASP B 200 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER B 206 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 265 removed outlier: 3.661A pdb=" N ALA B 231 " --> pdb=" O ASN B 227 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Proline residue: B 234 - end of helix removed outlier: 4.110A pdb=" N VAL B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 315 removed outlier: 4.842A pdb=" N VAL B 275 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE B 292 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA B 294 " --> pdb=" O GLN B 291 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG B 303 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET B 312 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP B 314 " --> pdb=" O GLN B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 381 Processing helix chain 'B' and resid 399 through 401 No H-bonds generated for 'chain 'B' and resid 399 through 401' Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 438 through 447 Processing helix chain 'B' and resid 451 through 454 No H-bonds generated for 'chain 'B' and resid 451 through 454' Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 475 through 488 Processing helix chain 'B' and resid 504 through 518 removed outlier: 3.768A pdb=" N ALA B 513 " --> pdb=" O LYS B 509 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 335 through 338 Processing sheet with id= B, first strand: chain 'A' and resid 538 through 541 Processing sheet with id= C, first strand: chain 'B' and resid 335 through 338 Processing sheet with id= D, first strand: chain 'B' and resid 538 through 541 550 hydrogen bonds defined for protein. 1414 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: 2.30 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 2962 1.36 - 1.50: 2174 1.50 - 1.64: 3656 1.64 - 1.77: 0 1.77 - 1.91: 94 Bond restraints: 8886 Sorted by residual: bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.38e+00 bond pdb=" C4 ADP A 601 " pdb=" C5 ADP A 601 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.37e+00 bond pdb=" CA PHE A 133 " pdb=" C PHE A 133 " ideal model delta sigma weight residual 1.524 1.511 0.013 1.28e-02 6.10e+03 1.06e+00 bond pdb=" CB PRO A 149 " pdb=" CG PRO A 149 " ideal model delta sigma weight residual 1.492 1.441 0.051 5.00e-02 4.00e+02 1.04e+00 bond pdb=" CB GLN B 512 " pdb=" CG GLN B 512 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.02e+00 ... (remaining 8881 not shown) Histogram of bond angle deviations from ideal: 99.48 - 106.80: 179 106.80 - 114.12: 5365 114.12 - 121.44: 4546 121.44 - 128.76: 1908 128.76 - 136.08: 62 Bond angle restraints: 12060 Sorted by residual: angle pdb=" CA GLN A 512 " pdb=" CB GLN A 512 " pdb=" CG GLN A 512 " ideal model delta sigma weight residual 114.10 120.28 -6.18 2.00e+00 2.50e-01 9.55e+00 angle pdb=" CA GLN B 512 " pdb=" CB GLN B 512 " pdb=" CG GLN B 512 " ideal model delta sigma weight residual 114.10 120.27 -6.17 2.00e+00 2.50e-01 9.52e+00 angle pdb=" CB MET B 24 " pdb=" CG MET B 24 " pdb=" SD MET B 24 " ideal model delta sigma weight residual 112.70 121.15 -8.45 3.00e+00 1.11e-01 7.94e+00 angle pdb=" CB MET A 24 " pdb=" CG MET A 24 " pdb=" SD MET A 24 " ideal model delta sigma weight residual 112.70 121.14 -8.44 3.00e+00 1.11e-01 7.92e+00 angle pdb=" CA GLY A 390 " pdb=" C GLY A 390 " pdb=" N ARG A 391 " ideal model delta sigma weight residual 114.75 117.22 -2.47 9.90e-01 1.02e+00 6.21e+00 ... (remaining 12055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.74: 4979 25.74 - 51.49: 297 51.49 - 77.23: 28 77.23 - 102.98: 0 102.98 - 128.72: 4 Dihedral angle restraints: 5308 sinusoidal: 2074 harmonic: 3234 Sorted by residual: dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual 300.00 171.28 128.72 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" O1B ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PB ADP B 601 " pdb=" PA ADP B 601 " ideal model delta sinusoidal sigma weight residual 300.00 171.30 128.70 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" C5' ADP A 601 " pdb=" O5' ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sinusoidal sigma weight residual 300.00 178.78 121.23 1 2.00e+01 2.50e-03 3.64e+01 ... (remaining 5305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 734 0.026 - 0.051: 399 0.051 - 0.077: 186 0.077 - 0.102: 75 0.102 - 0.128: 28 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA ILE A 492 " pdb=" N ILE A 492 " pdb=" C ILE A 492 " pdb=" CB ILE A 492 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE B 492 " pdb=" N ILE B 492 " pdb=" C ILE B 492 " pdb=" CB ILE B 492 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA VAL B 414 " pdb=" N VAL B 414 " pdb=" C VAL B 414 " pdb=" CB VAL B 414 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 1419 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 134 " 0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C MET A 134 " -0.058 2.00e-02 2.50e+03 pdb=" O MET A 134 " 0.022 2.00e-02 2.50e+03 pdb=" N ARG A 135 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 134 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C MET B 134 " 0.057 2.00e-02 2.50e+03 pdb=" O MET B 134 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG B 135 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 135 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" C ARG B 135 " -0.039 2.00e-02 2.50e+03 pdb=" O ARG B 135 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN B 136 " 0.013 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 255 2.71 - 3.26: 9635 3.26 - 3.81: 14294 3.81 - 4.35: 16701 4.35 - 4.90: 27966 Nonbonded interactions: 68851 Sorted by model distance: nonbonded pdb=" O SER B 458 " pdb=" OG1 THR B 463 " model vdw 2.164 2.440 nonbonded pdb=" O SER A 458 " pdb=" OG1 THR A 463 " model vdw 2.165 2.440 nonbonded pdb=" O GLU B 17 " pdb=" OG1 THR B 21 " model vdw 2.246 2.440 nonbonded pdb=" O GLU A 17 " pdb=" OG1 THR A 21 " model vdw 2.247 2.440 nonbonded pdb=" O ILE A 100 " pdb=" NE2 GLN B 209 " model vdw 2.318 2.520 ... (remaining 68846 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 251 or resid 253 through 556 or resid 601 throug \ h 602)) selection = (chain 'B' and (resid 1 through 251 or resid 253 through 556 or resid 601 throug \ h 602)) } 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=0.25 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 3.410 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 37.820 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 0.051 8886 Z= 0.234 Angle : 0.631 8.455 12060 Z= 0.325 Chirality : 0.041 0.128 1422 Planarity : 0.005 0.045 1530 Dihedral : 15.326 128.721 3212 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.13 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: 0.40 (0.26), residues: 1112 helix: 1.11 (0.20), residues: 706 sheet: -0.25 (0.56), residues: 80 loop : -1.41 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 8 HIS 0.005 0.001 HIS B 117 PHE 0.027 0.002 PHE B 133 TYR 0.015 0.002 TYR A 169 ARG 0.004 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.006 Fit side-chains REVERT: A 156 MET cc_start: 0.6351 (ptt) cc_final: 0.6052 (ptp) REVERT: B 156 MET cc_start: 0.6389 (ptt) cc_final: 0.6087 (ptp) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1695 time to fit residues: 43.6102 Evaluate side-chains 137 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8886 Z= 0.195 Angle : 0.606 6.947 12060 Z= 0.305 Chirality : 0.041 0.197 1422 Planarity : 0.004 0.040 1530 Dihedral : 7.466 99.057 1234 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.14 % Favored : 93.68 % Rotamer: Outliers : 1.52 % Allowed : 10.50 % Favored : 87.99 % 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: 0.50 (0.26), residues: 1112 helix: 1.16 (0.20), residues: 716 sheet: -0.19 (0.56), residues: 80 loop : -1.39 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 8 HIS 0.005 0.001 HIS B 117 PHE 0.023 0.001 PHE B 133 TYR 0.010 0.001 TYR B 169 ARG 0.007 0.000 ARG B 303 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 1.017 Fit side-chains REVERT: A 156 MET cc_start: 0.6492 (ptt) cc_final: 0.6253 (ptp) REVERT: A 278 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8285 (t80) REVERT: A 534 ARG cc_start: 0.6901 (OUTLIER) cc_final: 0.6116 (ptp-170) REVERT: A 541 PHE cc_start: 0.7391 (p90) cc_final: 0.7150 (p90) REVERT: B 156 MET cc_start: 0.6442 (ptt) cc_final: 0.6196 (ptp) REVERT: B 278 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8304 (t80) REVERT: B 534 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6129 (ptp-170) outliers start: 14 outliers final: 6 residues processed: 147 average time/residue: 0.1589 time to fit residues: 35.5226 Evaluate side-chains 145 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 278 PHE Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 534 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 89 optimal weight: 0.0270 chunk 99 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8886 Z= 0.197 Angle : 0.606 8.810 12060 Z= 0.305 Chirality : 0.041 0.184 1422 Planarity : 0.004 0.038 1530 Dihedral : 7.337 97.552 1234 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.68 % Favored : 93.14 % Rotamer: Outliers : 1.95 % Allowed : 12.12 % Favored : 85.93 % 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 (0.26), residues: 1112 helix: 1.15 (0.20), residues: 712 sheet: -0.39 (0.55), residues: 82 loop : -1.44 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 62 HIS 0.005 0.001 HIS A 117 PHE 0.024 0.002 PHE B 133 TYR 0.010 0.001 TYR A 169 ARG 0.006 0.000 ARG B 303 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 0.918 Fit side-chains REVERT: A 156 MET cc_start: 0.6516 (ptt) cc_final: 0.6267 (ptp) REVERT: A 278 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8481 (t80) REVERT: A 534 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6324 (ptp-170) REVERT: A 541 PHE cc_start: 0.7392 (p90) cc_final: 0.7159 (p90) REVERT: B 156 MET cc_start: 0.6514 (ptt) cc_final: 0.6260 (ptp) REVERT: B 278 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8485 (t80) REVERT: B 534 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.6394 (ptp-170) REVERT: B 541 PHE cc_start: 0.7365 (p90) cc_final: 0.7150 (p90) outliers start: 18 outliers final: 14 residues processed: 152 average time/residue: 0.1622 time to fit residues: 36.9704 Evaluate side-chains 158 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 140 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 278 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 534 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8886 Z= 0.261 Angle : 0.643 8.631 12060 Z= 0.325 Chirality : 0.042 0.174 1422 Planarity : 0.005 0.038 1530 Dihedral : 7.338 95.107 1234 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.86 % Favored : 92.96 % Rotamer: Outliers : 2.49 % Allowed : 12.66 % Favored : 84.85 % 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: 0.31 (0.26), residues: 1112 helix: 0.99 (0.20), residues: 716 sheet: -0.39 (0.51), residues: 82 loop : -1.37 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 8 HIS 0.005 0.001 HIS A 117 PHE 0.023 0.002 PHE B 133 TYR 0.016 0.002 TYR B 169 ARG 0.006 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 143 time to evaluate : 0.982 Fit side-chains REVERT: A 156 MET cc_start: 0.6568 (ptt) cc_final: 0.6307 (ptp) REVERT: A 278 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8713 (t80) REVERT: A 534 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6292 (ptp-170) REVERT: B 156 MET cc_start: 0.6572 (ptt) cc_final: 0.6308 (ptp) REVERT: B 278 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8716 (t80) REVERT: B 534 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6314 (ptp-170) outliers start: 23 outliers final: 14 residues processed: 154 average time/residue: 0.1673 time to fit residues: 37.9919 Evaluate side-chains 153 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 278 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 534 ARG Chi-restraints excluded: chain B residue 542 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 90 optimal weight: 20.0000 chunk 73 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN A 283 GLN B 232 GLN B 283 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8886 Z= 0.180 Angle : 0.618 8.003 12060 Z= 0.308 Chirality : 0.042 0.196 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.289 94.662 1234 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.59 % Favored : 93.23 % Rotamer: Outliers : 2.06 % Allowed : 13.64 % Favored : 84.31 % 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: 0.31 (0.26), residues: 1112 helix: 1.02 (0.20), residues: 714 sheet: -0.70 (0.49), residues: 84 loop : -1.32 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 62 HIS 0.006 0.001 HIS A 117 PHE 0.024 0.001 PHE A 133 TYR 0.012 0.001 TYR A 263 ARG 0.005 0.000 ARG B 303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 1.028 Fit side-chains REVERT: A 156 MET cc_start: 0.6530 (ptt) cc_final: 0.6280 (ptp) REVERT: A 534 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6140 (ptp-170) REVERT: B 156 MET cc_start: 0.6530 (ptt) cc_final: 0.6286 (ptp) REVERT: B 534 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6154 (ptp-170) outliers start: 19 outliers final: 14 residues processed: 150 average time/residue: 0.1766 time to fit residues: 40.5018 Evaluate side-chains 156 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 140 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 534 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8886 Z= 0.251 Angle : 0.658 8.531 12060 Z= 0.330 Chirality : 0.043 0.190 1422 Planarity : 0.005 0.038 1530 Dihedral : 7.336 94.801 1234 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.23 % Favored : 93.59 % Rotamer: Outliers : 2.06 % Allowed : 15.15 % Favored : 82.79 % 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: 0.21 (0.25), residues: 1112 helix: 0.91 (0.20), residues: 716 sheet: -0.63 (0.49), residues: 82 loop : -1.31 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 62 HIS 0.005 0.001 HIS A 117 PHE 0.023 0.002 PHE B 133 TYR 0.015 0.002 TYR A 169 ARG 0.005 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 1.094 Fit side-chains REVERT: A 62 TRP cc_start: 0.6869 (t-100) cc_final: 0.6610 (t-100) REVERT: A 156 MET cc_start: 0.6637 (ptt) cc_final: 0.6335 (ptp) REVERT: A 534 ARG cc_start: 0.6948 (OUTLIER) cc_final: 0.6049 (ptp-170) REVERT: A 541 PHE cc_start: 0.7232 (p90) cc_final: 0.6839 (p90) REVERT: B 62 TRP cc_start: 0.6867 (t-100) cc_final: 0.6611 (t-100) REVERT: B 156 MET cc_start: 0.6642 (ptt) cc_final: 0.6332 (ptp) REVERT: B 534 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6067 (ptp-170) outliers start: 19 outliers final: 17 residues processed: 153 average time/residue: 0.1634 time to fit residues: 37.9471 Evaluate side-chains 157 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 534 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 77 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 48 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8886 Z= 0.172 Angle : 0.625 8.295 12060 Z= 0.306 Chirality : 0.041 0.198 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.255 95.179 1234 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.32 % Favored : 93.50 % Rotamer: Outliers : 1.84 % Allowed : 15.37 % Favored : 82.79 % 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: 0.40 (0.26), residues: 1112 helix: 1.12 (0.20), residues: 710 sheet: -0.88 (0.49), residues: 84 loop : -1.27 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 62 HIS 0.005 0.001 HIS A 117 PHE 0.022 0.001 PHE B 133 TYR 0.011 0.001 TYR A 263 ARG 0.004 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 148 time to evaluate : 0.933 Fit side-chains REVERT: A 156 MET cc_start: 0.6559 (ptt) cc_final: 0.6319 (ptp) REVERT: B 156 MET cc_start: 0.6549 (ptt) cc_final: 0.6304 (ptp) outliers start: 17 outliers final: 14 residues processed: 150 average time/residue: 0.1844 time to fit residues: 39.5591 Evaluate side-chains 153 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 378 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8886 Z= 0.208 Angle : 0.646 8.568 12060 Z= 0.318 Chirality : 0.042 0.193 1422 Planarity : 0.004 0.038 1530 Dihedral : 7.230 96.346 1234 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.96 % Favored : 93.86 % Rotamer: Outliers : 1.62 % Allowed : 16.34 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.26), residues: 1112 helix: 1.05 (0.20), residues: 712 sheet: -0.83 (0.49), residues: 84 loop : -1.20 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 8 HIS 0.005 0.001 HIS A 117 PHE 0.022 0.002 PHE B 133 TYR 0.011 0.002 TYR B 169 ARG 0.005 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 1.037 Fit side-chains REVERT: A 41 LEU cc_start: 0.8912 (mm) cc_final: 0.8431 (mp) REVERT: A 156 MET cc_start: 0.6535 (ptt) cc_final: 0.6274 (ptp) REVERT: B 41 LEU cc_start: 0.8922 (mm) cc_final: 0.8443 (mp) REVERT: B 156 MET cc_start: 0.6549 (ptt) cc_final: 0.6291 (ptp) outliers start: 15 outliers final: 14 residues processed: 147 average time/residue: 0.1540 time to fit residues: 34.3966 Evaluate side-chains 157 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 378 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 0.0970 chunk 93 optimal weight: 0.0060 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8886 Z= 0.164 Angle : 0.627 8.763 12060 Z= 0.304 Chirality : 0.041 0.196 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.186 97.268 1234 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.05 % Favored : 93.77 % Rotamer: Outliers : 1.08 % Allowed : 16.56 % Favored : 82.36 % 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: 0.50 (0.26), residues: 1112 helix: 1.21 (0.20), residues: 708 sheet: -0.80 (0.50), residues: 84 loop : -1.25 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 106 HIS 0.005 0.001 HIS A 117 PHE 0.022 0.001 PHE A 133 TYR 0.014 0.001 TYR B 263 ARG 0.004 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 143 time to evaluate : 1.009 Fit side-chains REVERT: A 156 MET cc_start: 0.6563 (ptt) cc_final: 0.6303 (ptp) REVERT: B 156 MET cc_start: 0.6558 (ptt) cc_final: 0.6301 (ptp) outliers start: 10 outliers final: 10 residues processed: 145 average time/residue: 0.1656 time to fit residues: 36.3475 Evaluate side-chains 150 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 378 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 87 optimal weight: 0.0070 chunk 9 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 92 optimal weight: 0.0030 chunk 26 optimal weight: 10.0000 overall best weight: 0.4408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8886 Z= 0.160 Angle : 0.636 9.269 12060 Z= 0.306 Chirality : 0.041 0.198 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.159 97.983 1234 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.87 % Favored : 93.95 % Rotamer: Outliers : 0.97 % Allowed : 17.32 % Favored : 81.71 % 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 (0.26), residues: 1112 helix: 1.20 (0.20), residues: 712 sheet: -0.71 (0.52), residues: 84 loop : -1.16 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 106 HIS 0.005 0.001 HIS A 117 PHE 0.022 0.001 PHE A 133 TYR 0.008 0.001 TYR A 211 ARG 0.004 0.000 ARG B 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 151 time to evaluate : 0.889 Fit side-chains REVERT: A 156 MET cc_start: 0.6477 (ptt) cc_final: 0.6223 (ptp) REVERT: B 156 MET cc_start: 0.6474 (ptt) cc_final: 0.6216 (ptp) outliers start: 9 outliers final: 9 residues processed: 153 average time/residue: 0.1567 time to fit residues: 36.6428 Evaluate side-chains 153 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 378 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 89 optimal weight: 0.0570 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 63 optimal weight: 4.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.150759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.120621 restraints weight = 110061.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.128263 restraints weight = 27977.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.135076 restraints weight = 10156.559| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8886 Z= 0.169 Angle : 0.643 8.538 12060 Z= 0.309 Chirality : 0.041 0.201 1422 Planarity : 0.004 0.038 1530 Dihedral : 7.159 98.897 1234 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.96 % Favored : 93.86 % Rotamer: Outliers : 1.19 % Allowed : 18.40 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.26), residues: 1112 helix: 1.19 (0.20), residues: 710 sheet: -0.70 (0.52), residues: 84 loop : -1.21 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 106 HIS 0.005 0.001 HIS A 117 PHE 0.030 0.001 PHE B 295 TYR 0.009 0.001 TYR B 7 ARG 0.004 0.000 ARG B 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1911.14 seconds wall clock time: 35 minutes 27.31 seconds (2127.31 seconds total)