Starting phenix.real_space_refine on Tue Nov 14 13:26:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo9_14844/11_2023/7zo9_14844_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo9_14844/11_2023/7zo9_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_14844/11_2023/7zo9_14844.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo9_14844/11_2023/7zo9_14844.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo9_14844/11_2023/7zo9_14844_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo9_14844/11_2023/7zo9_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-1.21rc1-5144/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: 12.95, per 1000 atoms: 1.48 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: 3.99 Conformation dependent library (CDL) restraints added in 4.7 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: 1.71 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: 2.41 Time building geometry restraints manager: 4.24 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: 0.710 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: 0.010 Extract box with map and model: 3.410 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 39.470 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.250 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.043 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1707 time to fit residues: 43.4755 Evaluate side-chains 137 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.935 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2773 ------------------------------------------------------------------------------- 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: 0.7724 moved from start: 0.0828 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 6.868 12060 Z= 0.305 Chirality : 0.041 0.195 1422 Planarity : 0.004 0.040 1530 Dihedral : 7.484 100.203 1234 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.29 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: 0.48 (0.26), residues: 1112 helix: 1.13 (0.20), residues: 718 sheet: -0.18 (0.56), residues: 80 loop : -1.39 (0.36), residues: 314 *********************** 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 : 1.118 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 147 average time/residue: 0.1692 time to fit residues: 37.5168 Evaluate side-chains 141 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 135 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0859 time to fit residues: 2.3846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 0.3980 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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: 0.7712 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8886 Z= 0.183 Angle : 0.602 8.543 12060 Z= 0.302 Chirality : 0.041 0.186 1422 Planarity : 0.004 0.038 1530 Dihedral : 7.344 97.814 1234 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.50 % Favored : 93.32 % Rotamer: Outliers : 1.30 % Allowed : 12.45 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1112 helix: 1.18 (0.20), residues: 710 sheet: -0.40 (0.54), residues: 82 loop : -1.41 (0.35), residues: 320 *********************** 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 154 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.023 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 146 average time/residue: 0.1635 time to fit residues: 35.9079 Evaluate side-chains 144 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 1.022 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0907 time to fit residues: 2.7657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.7771 moved from start: 0.1280 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= 0.243 Angle : 0.645 8.652 12060 Z= 0.323 Chirality : 0.042 0.172 1422 Planarity : 0.004 0.038 1530 Dihedral : 7.328 95.283 1234 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.04 % Favored : 92.78 % Rotamer: Outliers : 1.08 % Allowed : 14.18 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1112 helix: 1.02 (0.20), residues: 718 sheet: -0.51 (0.50), residues: 82 loop : -1.27 (0.35), residues: 312 *********************** 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 154 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 1.084 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 145 average time/residue: 0.1834 time to fit residues: 39.2222 Evaluate side-chains 144 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 138 time to evaluate : 1.004 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0985 time to fit residues: 2.4072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 43 optimal weight: 0.0010 chunk 90 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 26 optimal weight: 0.0070 overall best weight: 0.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 232 GLN B 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8886 Z= 0.167 Angle : 0.615 8.141 12060 Z= 0.302 Chirality : 0.041 0.192 1422 Planarity : 0.004 0.040 1530 Dihedral : 7.236 95.383 1234 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.59 % Favored : 93.23 % Rotamer: Outliers : 0.54 % Allowed : 14.29 % Favored : 85.17 % 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: 0.48 (0.26), residues: 1112 helix: 1.18 (0.20), residues: 712 sheet: -0.72 (0.49), residues: 84 loop : -1.29 (0.35), residues: 316 *********************** 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 143 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 138 time to evaluate : 1.076 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 141 average time/residue: 0.1796 time to fit residues: 37.9472 Evaluate side-chains 142 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 1.025 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1207 time to fit residues: 2.3747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8886 Z= 0.205 Angle : 0.634 8.000 12060 Z= 0.313 Chirality : 0.042 0.189 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.246 96.122 1234 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.32 % Favored : 93.50 % Rotamer: Outliers : 0.32 % Allowed : 16.13 % Favored : 83.55 % 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: 0.48 (0.26), residues: 1112 helix: 1.13 (0.20), residues: 714 sheet: -0.64 (0.50), residues: 84 loop : -1.19 (0.36), residues: 314 *********************** 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 146 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 1.050 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 143 average time/residue: 0.1678 time to fit residues: 35.8109 Evaluate side-chains 139 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0947 time to fit residues: 1.6366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.6980 chunk 60 optimal weight: 0.0060 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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: 0.7694 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8886 Z= 0.169 Angle : 0.624 8.232 12060 Z= 0.304 Chirality : 0.041 0.196 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.186 97.005 1234 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.23 % Favored : 93.59 % Rotamer: Outliers : 0.32 % Allowed : 16.67 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1112 helix: 1.26 (0.20), residues: 708 sheet: -0.66 (0.51), residues: 84 loop : -1.28 (0.36), residues: 320 *********************** 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 146 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 1.014 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 143 average time/residue: 0.1880 time to fit residues: 39.0381 Evaluate side-chains 139 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 1.061 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0851 time to fit residues: 1.7700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 20 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 92 optimal weight: 0.0570 overall best weight: 1.3104 ------------------------------------------------------------------------------- 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: 0.7771 moved from start: 0.1810 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= 0.241 Angle : 0.674 9.189 12060 Z= 0.330 Chirality : 0.043 0.186 1422 Planarity : 0.004 0.038 1530 Dihedral : 7.239 97.950 1234 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.23 % Favored : 93.59 % Rotamer: Outliers : 0.54 % Allowed : 17.64 % Favored : 81.82 % 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: 0.42 (0.26), residues: 1112 helix: 1.07 (0.20), residues: 714 sheet: -0.67 (0.51), residues: 84 loop : -1.20 (0.36), residues: 314 *********************** 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 150 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 145 time to evaluate : 0.943 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 145 average time/residue: 0.1800 time to fit residues: 38.7156 Evaluate side-chains 146 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 1.016 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0961 time to fit residues: 2.0290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 59 optimal weight: 0.0970 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 0.0770 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 104 optimal weight: 0.0470 chunk 63 optimal weight: 1.9990 overall best weight: 0.3634 ------------------------------------------------------------------------------- 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: 0.7671 moved from start: 0.2006 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= 0.158 Angle : 0.632 8.820 12060 Z= 0.304 Chirality : 0.041 0.208 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.174 98.862 1234 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.96 % Favored : 93.86 % Rotamer: Outliers : 0.43 % Allowed : 17.64 % Favored : 81.93 % 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: 0.58 (0.26), residues: 1112 helix: 1.30 (0.20), residues: 706 sheet: -0.71 (0.51), residues: 84 loop : -1.29 (0.36), residues: 322 *********************** 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 160 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 156 time to evaluate : 1.040 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 156 average time/residue: 0.1732 time to fit residues: 39.8653 Evaluate side-chains 154 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 150 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0791 time to fit residues: 1.9250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.0970 chunk 72 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 0.0050 chunk 53 optimal weight: 0.0470 chunk 69 optimal weight: 0.9980 chunk 92 optimal weight: 0.1980 chunk 26 optimal weight: 0.7980 overall best weight: 0.2290 ------------------------------------------------------------------------------- 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 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2154 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= 0.152 Angle : 0.636 9.179 12060 Z= 0.304 Chirality : 0.041 0.204 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.137 99.576 1234 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.87 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 18.72 % Favored : 81.28 % 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: 0.64 (0.26), residues: 1112 helix: 1.31 (0.20), residues: 704 sheet: -0.73 (0.51), residues: 84 loop : -1.14 (0.36), residues: 324 ********************** 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 159 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.988 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1763 time to fit residues: 41.3148 Evaluate side-chains 150 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.149708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.117500 restraints weight = 109976.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.124409 restraints weight = 23935.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.129077 restraints weight = 10852.101| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8886 Z= 0.209 Angle : 0.637 8.163 12060 Z= 0.313 Chirality : 0.042 0.192 1422 Planarity : 0.004 0.038 1530 Dihedral : 7.167 101.902 1234 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.60 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 18.94 % Favored : 81.06 % 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: 1.22 (0.20), residues: 708 sheet: -0.67 (0.52), residues: 84 loop : -1.17 (0.36), residues: 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1943.30 seconds wall clock time: 36 minutes 8.18 seconds (2168.18 seconds total)