Starting phenix.real_space_refine on Thu Jul 31 13:31:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bah_15948/07_2025/8bah_15948.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bah_15948/07_2025/8bah_15948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bah_15948/07_2025/8bah_15948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bah_15948/07_2025/8bah_15948.map" model { file = "/net/cci-nas-00/data/ceres_data/8bah_15948/07_2025/8bah_15948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bah_15948/07_2025/8bah_15948.cif" } resolution = 4.13 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= 0.012 sd= 0.095 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 Mn 4 7.51 5 S 30 5.16 5 C 4382 2.51 5 N 1193 2.21 5 O 1265 1.98 5 H 6801 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13675 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6381 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain: "B" Number of atoms: 6370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 6370 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 20, 'TRANS': 377} Chain: "C" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 920 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.23, per 1000 atoms: 0.53 Number of scatterers: 13675 At special positions: 0 Unit cell: (109.077, 84.72, 91.074, 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) Mn 4 24.99 S 30 16.00 O 1265 8.00 N 1193 7.00 C 4382 6.00 H 6801 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 1.1 seconds 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1606 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 11 sheets defined 32.4% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 68 through 84 removed outlier: 3.760A pdb=" N MET A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 101 Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 139 through 148 Processing helix chain 'A' and resid 185 through 195 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.689A pdb=" N TRP A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 234 Processing helix chain 'A' and resid 275 through 280 removed outlier: 4.123A pdb=" N VAL A 280 " --> pdb=" O PRO A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 327 through 353 removed outlier: 4.291A pdb=" N GLY A 353 " --> pdb=" O ARG A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 383 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 391 through 394 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 68 through 84 removed outlier: 3.644A pdb=" N MET B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 102 removed outlier: 4.134A pdb=" N ASN B 100 " --> pdb=" O ASP B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 139 through 148 Processing helix chain 'B' and resid 185 through 195 Processing helix chain 'B' and resid 206 through 210 removed outlier: 3.816A pdb=" N TRP B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 234 Processing helix chain 'B' and resid 275 through 280 removed outlier: 4.089A pdb=" N VAL B 280 " --> pdb=" O PRO B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 327 through 352 Processing helix chain 'B' and resid 377 through 383 Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 391 through 394 Processing helix chain 'C' and resid 704 through 706 No H-bonds generated for 'chain 'C' and resid 704 through 706' Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.492A pdb=" N VAL A 122 " --> pdb=" O ASN A 151 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS A 14 " --> pdb=" O PHE A 54 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU A 56 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU A 16 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 93 removed outlier: 3.618A pdb=" N PHE A 211 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASN A 212 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE A 242 " --> pdb=" O ASN A 212 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N PHE A 214 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 241 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE A 263 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA A 252 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN A 265 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 164 Processing sheet with id=AA4, first strand: chain 'A' and resid 202 through 203 removed outlier: 5.365A pdb=" N ARG A 202 " --> pdb=" O ARG C 660 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 313 Processing sheet with id=AA6, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.657A pdb=" N VAL B 122 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE B 55 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS B 14 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU B 56 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU B 16 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.657A pdb=" N VAL B 122 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE B 55 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS B 14 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU B 56 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU B 16 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 92 through 93 removed outlier: 3.712A pdb=" N PHE B 211 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL B 241 " --> pdb=" O SER B 264 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE B 263 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 252 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN B 265 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 162 through 163 removed outlier: 6.405A pdb=" N ILE B 162 " --> pdb=" O THR B 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AB2, first strand: chain 'B' and resid 307 through 313 removed outlier: 6.643A pdb=" N PHE B 308 " --> pdb=" O ARG B 364 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ARG B 366 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU B 310 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ASP B 368 " --> pdb=" O GLU B 310 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE B 312 " --> pdb=" O ASP B 368 " (cutoff:3.500A) 234 hydrogen bonds defined for protein. 612 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.26 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6789 1.03 - 1.23: 12 1.23 - 1.42: 2960 1.42 - 1.61: 4022 1.61 - 1.81: 48 Bond restraints: 13831 Sorted by residual: bond pdb=" N ASN C 666 " pdb=" CA ASN C 666 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.62e+00 bond pdb=" N SER C 669 " pdb=" CA SER C 669 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.22e-02 6.72e+03 8.02e+00 bond pdb=" N THR C 668 " pdb=" CA THR C 668 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.22e-02 6.72e+03 7.46e+00 bond pdb=" N HIS B 247 " pdb=" CA HIS B 247 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.33e-02 5.65e+03 6.67e+00 bond pdb=" CA SER B 119 " pdb=" CB SER B 119 " ideal model delta sigma weight residual 1.532 1.494 0.039 1.53e-02 4.27e+03 6.35e+00 ... (remaining 13826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 21293 1.28 - 2.56: 2084 2.56 - 3.84: 1556 3.84 - 5.12: 75 5.12 - 6.40: 19 Bond angle restraints: 25027 Sorted by residual: angle pdb=" CA SER B 119 " pdb=" C SER B 119 " pdb=" O SER B 119 " ideal model delta sigma weight residual 119.41 114.41 5.00 1.13e+00 7.83e-01 1.96e+01 angle pdb=" C SER B 119 " pdb=" CA SER B 119 " pdb=" CB SER B 119 " ideal model delta sigma weight residual 109.24 115.64 -6.40 1.75e+00 3.27e-01 1.34e+01 angle pdb=" CA ASN C 666 " pdb=" C ASN C 666 " pdb=" O ASN C 666 " ideal model delta sigma weight residual 121.50 117.02 4.48 1.25e+00 6.40e-01 1.28e+01 angle pdb=" CA SER C 669 " pdb=" C SER C 669 " pdb=" O SER C 669 " ideal model delta sigma weight residual 121.16 117.39 3.77 1.12e+00 7.97e-01 1.13e+01 angle pdb=" CA SER C 667 " pdb=" C SER C 667 " pdb=" O SER C 667 " ideal model delta sigma weight residual 120.51 115.75 4.76 1.43e+00 4.89e-01 1.11e+01 ... (remaining 25022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.63: 5914 13.63 - 27.26: 364 27.26 - 40.88: 134 40.88 - 54.51: 77 54.51 - 68.14: 15 Dihedral angle restraints: 6504 sinusoidal: 3536 harmonic: 2968 Sorted by residual: dihedral pdb=" CA ASP A 131 " pdb=" CB ASP A 131 " pdb=" CG ASP A 131 " pdb=" OD1 ASP A 131 " ideal model delta sinusoidal sigma weight residual -30.00 -88.46 58.46 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP B 235 " pdb=" CB ASP B 235 " pdb=" CG ASP B 235 " pdb=" OD1 ASP B 235 " ideal model delta sinusoidal sigma weight residual -30.00 -85.44 55.44 1 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CA CYS A 83 " pdb=" CB CYS A 83 " pdb=" SG CYS A 83 " pdb=" HG CYS A 83 " ideal model delta sinusoidal sigma weight residual -60.00 -107.89 47.89 3 1.50e+01 4.44e-03 8.56e+00 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 864 0.051 - 0.102: 119 0.102 - 0.153: 50 0.153 - 0.204: 0 0.204 - 0.255: 2 Chirality restraints: 1035 Sorted by residual: chirality pdb=" CA SER B 119 " pdb=" N SER B 119 " pdb=" C SER B 119 " pdb=" CB SER B 119 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA VAL C 663 " pdb=" N VAL C 663 " pdb=" C VAL C 663 " pdb=" CB VAL C 663 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA THR C 668 " pdb=" N THR C 668 " pdb=" C THR C 668 " pdb=" CB THR C 668 " both_signs ideal model delta sigma weight residual False 2.53 2.67 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 1032 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 660 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C ARG C 660 " -0.051 2.00e-02 2.50e+03 pdb=" O ARG C 660 " 0.019 2.00e-02 2.50e+03 pdb=" N SER C 661 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 247 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C HIS B 247 " -0.046 2.00e-02 2.50e+03 pdb=" O HIS B 247 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU B 248 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 664 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C ILE C 664 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE C 664 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS C 665 " 0.010 2.00e-02 2.50e+03 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 404 2.11 - 2.73: 25068 2.73 - 3.36: 39252 3.36 - 3.98: 49819 3.98 - 4.60: 78278 Nonbonded interactions: 192821 Sorted by model distance: nonbonded pdb=" H ASN B 110 " pdb=" OD1 ASN B 151 " model vdw 1.489 2.450 nonbonded pdb=" OD1 ASP A 9 " pdb=" HG1 THR A 12 " model vdw 1.508 2.450 nonbonded pdb=" O SER A 68 " pdb=" HG1 THR A 71 " model vdw 1.516 2.450 nonbonded pdb=" OE2 GLU B 27 " pdb=" HZ3 LYS B 70 " model vdw 1.527 2.450 nonbonded pdb=" O CYS B 139 " pdb=" H ASP B 142 " model vdw 1.534 2.450 ... (remaining 192816 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG \ 22 or name HG23)) or resid 4 through 400 or resid 801 through 802)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.230 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 32.960 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 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 0.039 7030 Z= 0.200 Angle : 0.537 6.397 9497 Z= 0.316 Chirality : 0.043 0.255 1035 Planarity : 0.004 0.036 1246 Dihedral : 10.657 68.141 2632 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.29), residues: 849 helix: 1.70 (0.37), residues: 205 sheet: -0.48 (0.39), residues: 169 loop : 0.29 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 210 HIS 0.003 0.000 HIS B 63 PHE 0.012 0.001 PHE C 688 TYR 0.007 0.001 TYR A 82 ARG 0.003 0.000 ARG B 380 Details of bonding type rmsd hydrogen bonds : bond 0.18417 ( 228) hydrogen bonds : angle 7.65902 ( 612) covalent geometry : bond 0.00341 ( 7030) covalent geometry : angle 0.53713 ( 9497) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.7535 (m-70) cc_final: 0.6872 (m170) REVERT: A 274 LEU cc_start: 0.8264 (mt) cc_final: 0.7557 (mt) REVERT: A 294 MET cc_start: 0.9114 (ppp) cc_final: 0.8465 (ppp) REVERT: A 308 PHE cc_start: 0.8440 (m-80) cc_final: 0.8185 (m-10) REVERT: A 366 ARG cc_start: 0.8728 (mtp180) cc_final: 0.8500 (mtm-85) REVERT: A 391 ASN cc_start: 0.8404 (p0) cc_final: 0.8072 (p0) REVERT: B 359 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6767 (mm-30) REVERT: B 391 ASN cc_start: 0.8566 (p0) cc_final: 0.8313 (p0) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.4044 time to fit residues: 105.3151 Evaluate side-chains 154 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.123096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.091711 restraints weight = 45638.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.096503 restraints weight = 21653.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.099836 restraints weight = 13617.475| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7030 Z= 0.189 Angle : 0.525 4.129 9497 Z= 0.285 Chirality : 0.043 0.167 1035 Planarity : 0.004 0.041 1246 Dihedral : 4.538 15.587 908 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.29), residues: 849 helix: 1.86 (0.37), residues: 206 sheet: -0.77 (0.37), residues: 180 loop : -0.02 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 210 HIS 0.004 0.001 HIS B 217 PHE 0.012 0.001 PHE C 688 TYR 0.012 0.001 TYR B 179 ARG 0.004 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 228) hydrogen bonds : angle 5.61979 ( 612) covalent geometry : bond 0.00391 ( 7030) covalent geometry : angle 0.52498 ( 9497) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.7994 (m-70) cc_final: 0.7091 (m170) REVERT: A 274 LEU cc_start: 0.8174 (mt) cc_final: 0.7739 (mt) REVERT: A 308 PHE cc_start: 0.8512 (m-80) cc_final: 0.8179 (m-10) REVERT: A 366 ARG cc_start: 0.8912 (mtp180) cc_final: 0.8536 (mtm-85) REVERT: B 42 GLU cc_start: 0.8989 (tt0) cc_final: 0.8768 (tt0) REVERT: B 129 ASN cc_start: 0.8956 (m-40) cc_final: 0.8626 (m-40) REVERT: B 359 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6891 (mm-30) REVERT: B 391 ASN cc_start: 0.8513 (p0) cc_final: 0.8169 (p0) REVERT: C 693 TYR cc_start: 0.7410 (p90) cc_final: 0.7130 (p90) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.4993 time to fit residues: 121.6402 Evaluate side-chains 149 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 15 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.121704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.089872 restraints weight = 46934.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.094652 restraints weight = 22415.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.097914 restraints weight = 14209.221| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7030 Z= 0.202 Angle : 0.517 4.116 9497 Z= 0.279 Chirality : 0.042 0.150 1035 Planarity : 0.004 0.044 1246 Dihedral : 4.619 15.487 908 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.29), residues: 849 helix: 1.99 (0.37), residues: 200 sheet: -0.93 (0.36), residues: 186 loop : -0.16 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 210 HIS 0.005 0.001 HIS C 711 PHE 0.012 0.001 PHE B 54 TYR 0.011 0.001 TYR B 179 ARG 0.003 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 228) hydrogen bonds : angle 5.31471 ( 612) covalent geometry : bond 0.00417 ( 7030) covalent geometry : angle 0.51692 ( 9497) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.7920 (m-70) cc_final: 0.7020 (m170) REVERT: A 42 GLU cc_start: 0.8526 (tt0) cc_final: 0.8148 (mt-10) REVERT: A 64 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7841 (mt-10) REVERT: A 142 ASP cc_start: 0.9326 (m-30) cc_final: 0.9113 (m-30) REVERT: A 176 ILE cc_start: 0.8174 (mt) cc_final: 0.7952 (mt) REVERT: A 219 ASN cc_start: 0.7907 (m-40) cc_final: 0.7229 (t0) REVERT: A 274 LEU cc_start: 0.8141 (mt) cc_final: 0.7770 (mt) REVERT: A 294 MET cc_start: 0.9163 (ppp) cc_final: 0.8413 (ppp) REVERT: A 308 PHE cc_start: 0.8511 (m-80) cc_final: 0.8204 (m-10) REVERT: A 366 ARG cc_start: 0.8968 (mtp180) cc_final: 0.8484 (mtm-85) REVERT: B 128 ASN cc_start: 0.8523 (p0) cc_final: 0.8264 (p0) REVERT: B 129 ASN cc_start: 0.8912 (m-40) cc_final: 0.8547 (m-40) REVERT: B 391 ASN cc_start: 0.8668 (p0) cc_final: 0.8156 (p0) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.4377 time to fit residues: 106.8125 Evaluate side-chains 147 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN B 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.121261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.089785 restraints weight = 46311.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.094563 restraints weight = 22208.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.097853 restraints weight = 14114.372| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7030 Z= 0.213 Angle : 0.524 5.958 9497 Z= 0.283 Chirality : 0.042 0.149 1035 Planarity : 0.004 0.044 1246 Dihedral : 4.671 15.364 908 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: 0.05 (0.29), residues: 849 helix: 1.95 (0.38), residues: 200 sheet: -1.14 (0.37), residues: 174 loop : -0.28 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 210 HIS 0.005 0.001 HIS B 126 PHE 0.013 0.001 PHE B 54 TYR 0.010 0.001 TYR B 179 ARG 0.003 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.03264 ( 228) hydrogen bonds : angle 5.18778 ( 612) covalent geometry : bond 0.00443 ( 7030) covalent geometry : angle 0.52361 ( 9497) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8547 (tt0) cc_final: 0.8280 (mt-10) REVERT: A 64 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7731 (mt-10) REVERT: A 274 LEU cc_start: 0.8162 (mt) cc_final: 0.7749 (mt) REVERT: A 294 MET cc_start: 0.9170 (ppp) cc_final: 0.8413 (ppp) REVERT: A 308 PHE cc_start: 0.8505 (m-80) cc_final: 0.8205 (m-10) REVERT: A 366 ARG cc_start: 0.8950 (mtp180) cc_final: 0.8388 (mtm-85) REVERT: B 128 ASN cc_start: 0.8633 (p0) cc_final: 0.8379 (p0) REVERT: B 129 ASN cc_start: 0.8928 (m-40) cc_final: 0.8538 (m-40) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.5106 time to fit residues: 124.4253 Evaluate side-chains 138 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 23 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.120344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.088733 restraints weight = 47239.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.093449 restraints weight = 22853.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.096731 restraints weight = 14636.737| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7030 Z= 0.242 Angle : 0.549 4.505 9497 Z= 0.299 Chirality : 0.042 0.151 1035 Planarity : 0.004 0.045 1246 Dihedral : 4.831 15.985 908 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: -0.16 (0.29), residues: 849 helix: 1.77 (0.37), residues: 205 sheet: -1.25 (0.37), residues: 186 loop : -0.40 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 210 HIS 0.004 0.001 HIS B 217 PHE 0.014 0.002 PHE B 54 TYR 0.010 0.002 TYR B 179 ARG 0.003 0.000 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 228) hydrogen bonds : angle 5.18387 ( 612) covalent geometry : bond 0.00495 ( 7030) covalent geometry : angle 0.54878 ( 9497) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.7688 (m170) cc_final: 0.7076 (m170) REVERT: A 42 GLU cc_start: 0.8521 (tt0) cc_final: 0.8221 (mt-10) REVERT: A 64 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7698 (mt-10) REVERT: A 142 ASP cc_start: 0.9332 (m-30) cc_final: 0.9093 (m-30) REVERT: A 219 ASN cc_start: 0.7995 (m-40) cc_final: 0.7270 (t0) REVERT: A 274 LEU cc_start: 0.8274 (mt) cc_final: 0.7858 (mt) REVERT: A 306 GLN cc_start: 0.7604 (mp10) cc_final: 0.7211 (mp10) REVERT: A 308 PHE cc_start: 0.8501 (m-80) cc_final: 0.8203 (m-10) REVERT: A 366 ARG cc_start: 0.8978 (mtp180) cc_final: 0.8308 (mtm-85) REVERT: B 82 TYR cc_start: 0.8501 (m-10) cc_final: 0.8145 (m-10) REVERT: B 128 ASN cc_start: 0.8749 (p0) cc_final: 0.8520 (p0) REVERT: B 129 ASN cc_start: 0.8887 (m-40) cc_final: 0.8518 (m-40) REVERT: C 699 LEU cc_start: 0.8349 (tt) cc_final: 0.7873 (pp) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.5033 time to fit residues: 114.8576 Evaluate side-chains 139 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 15 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 0.0980 chunk 45 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.123496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.091884 restraints weight = 45874.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.096887 restraints weight = 21452.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.100266 restraints weight = 13427.422| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7030 Z= 0.095 Angle : 0.463 4.352 9497 Z= 0.242 Chirality : 0.043 0.154 1035 Planarity : 0.004 0.043 1246 Dihedral : 4.419 14.940 908 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.29), residues: 849 helix: 2.17 (0.38), residues: 206 sheet: -0.97 (0.37), residues: 181 loop : -0.30 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 108 HIS 0.004 0.001 HIS A 356 PHE 0.011 0.001 PHE A 307 TYR 0.011 0.001 TYR B 179 ARG 0.002 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.02771 ( 228) hydrogen bonds : angle 4.65753 ( 612) covalent geometry : bond 0.00210 ( 7030) covalent geometry : angle 0.46300 ( 9497) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8513 (tt0) cc_final: 0.8235 (mt-10) REVERT: A 64 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7647 (mt-10) REVERT: A 142 ASP cc_start: 0.9298 (m-30) cc_final: 0.9060 (m-30) REVERT: A 274 LEU cc_start: 0.8217 (mt) cc_final: 0.7786 (mt) REVERT: A 308 PHE cc_start: 0.8461 (m-80) cc_final: 0.8181 (m-10) REVERT: A 366 ARG cc_start: 0.8965 (mtp180) cc_final: 0.8323 (mtm-85) REVERT: B 42 GLU cc_start: 0.9056 (tt0) cc_final: 0.8816 (tt0) REVERT: B 82 TYR cc_start: 0.8416 (m-10) cc_final: 0.8068 (m-10) REVERT: B 129 ASN cc_start: 0.8912 (m-40) cc_final: 0.8502 (m-40) REVERT: B 190 TYR cc_start: 0.8325 (t80) cc_final: 0.8066 (t80) REVERT: B 359 GLU cc_start: 0.7380 (mm-30) cc_final: 0.6853 (mm-30) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.6627 time to fit residues: 167.9964 Evaluate side-chains 153 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.121215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.090107 restraints weight = 46569.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.094908 restraints weight = 21871.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.098259 restraints weight = 13742.732| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7030 Z= 0.162 Angle : 0.489 4.298 9497 Z= 0.259 Chirality : 0.042 0.147 1035 Planarity : 0.004 0.042 1246 Dihedral : 4.486 15.791 908 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: 0.16 (0.30), residues: 849 helix: 2.20 (0.38), residues: 200 sheet: -1.08 (0.37), residues: 182 loop : -0.26 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 210 HIS 0.004 0.001 HIS A 22 PHE 0.010 0.001 PHE B 399 TYR 0.010 0.001 TYR B 179 ARG 0.002 0.000 ARG B 400 Details of bonding type rmsd hydrogen bonds : bond 0.02847 ( 228) hydrogen bonds : angle 4.78508 ( 612) covalent geometry : bond 0.00341 ( 7030) covalent geometry : angle 0.48896 ( 9497) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8470 (tt0) cc_final: 0.8214 (mt-10) REVERT: A 64 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7679 (mt-10) REVERT: A 219 ASN cc_start: 0.7958 (m-40) cc_final: 0.7257 (t0) REVERT: A 274 LEU cc_start: 0.8272 (mt) cc_final: 0.7941 (mt) REVERT: A 298 LYS cc_start: 0.9173 (pttt) cc_final: 0.8889 (ptpp) REVERT: A 308 PHE cc_start: 0.8479 (m-80) cc_final: 0.8198 (m-10) REVERT: A 366 ARG cc_start: 0.8963 (mtp180) cc_final: 0.8322 (mtm-85) REVERT: B 82 TYR cc_start: 0.8458 (m-10) cc_final: 0.8096 (m-10) REVERT: B 129 ASN cc_start: 0.8838 (m-40) cc_final: 0.8553 (m-40) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.4846 time to fit residues: 109.4296 Evaluate side-chains 143 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 48 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.120791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.089856 restraints weight = 46566.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.094583 restraints weight = 21943.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.097860 restraints weight = 13847.386| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7030 Z= 0.168 Angle : 0.488 4.387 9497 Z= 0.261 Chirality : 0.042 0.145 1035 Planarity : 0.004 0.042 1246 Dihedral : 4.528 15.372 908 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.29), residues: 849 helix: 2.14 (0.38), residues: 206 sheet: -1.12 (0.37), residues: 187 loop : -0.50 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.003 0.001 HIS B 126 PHE 0.014 0.002 PHE A 307 TYR 0.011 0.001 TYR B 179 ARG 0.002 0.000 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.02858 ( 228) hydrogen bonds : angle 4.76467 ( 612) covalent geometry : bond 0.00352 ( 7030) covalent geometry : angle 0.48781 ( 9497) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8431 (tt0) cc_final: 0.8159 (mt-10) REVERT: A 64 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7705 (mt-10) REVERT: A 142 ASP cc_start: 0.9335 (m-30) cc_final: 0.9100 (m-30) REVERT: A 219 ASN cc_start: 0.8017 (m-40) cc_final: 0.7323 (t0) REVERT: A 308 PHE cc_start: 0.8485 (m-80) cc_final: 0.8212 (m-10) REVERT: A 366 ARG cc_start: 0.9009 (mtp180) cc_final: 0.8354 (mtm-85) REVERT: B 129 ASN cc_start: 0.8744 (m-40) cc_final: 0.8432 (m-40) REVERT: B 391 ASN cc_start: 0.8750 (p0) cc_final: 0.8212 (p0) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.4071 time to fit residues: 93.2845 Evaluate side-chains 140 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 0.0370 chunk 13 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.123375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.092416 restraints weight = 45187.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.097344 restraints weight = 20935.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.100667 restraints weight = 13056.345| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7030 Z= 0.092 Angle : 0.458 4.212 9497 Z= 0.238 Chirality : 0.043 0.156 1035 Planarity : 0.004 0.041 1246 Dihedral : 4.280 14.537 908 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 0.26 (0.30), residues: 849 helix: 2.41 (0.38), residues: 205 sheet: -0.90 (0.37), residues: 186 loop : -0.35 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 108 HIS 0.003 0.001 HIS B 126 PHE 0.019 0.001 PHE B 91 TYR 0.012 0.001 TYR B 179 ARG 0.003 0.000 ARG B 366 Details of bonding type rmsd hydrogen bonds : bond 0.02671 ( 228) hydrogen bonds : angle 4.43074 ( 612) covalent geometry : bond 0.00211 ( 7030) covalent geometry : angle 0.45834 ( 9497) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8461 (tt0) cc_final: 0.8223 (mt-10) REVERT: A 64 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7731 (mt-10) REVERT: A 142 ASP cc_start: 0.9312 (m-30) cc_final: 0.9084 (m-30) REVERT: A 219 ASN cc_start: 0.7972 (m-40) cc_final: 0.7245 (t0) REVERT: A 274 LEU cc_start: 0.8365 (mt) cc_final: 0.7944 (mt) REVERT: A 308 PHE cc_start: 0.8432 (m-80) cc_final: 0.8169 (m-10) REVERT: A 366 ARG cc_start: 0.9015 (mtp180) cc_final: 0.8367 (mtm-85) REVERT: B 129 ASN cc_start: 0.8787 (m-40) cc_final: 0.8454 (m-40) REVERT: B 190 TYR cc_start: 0.8330 (t80) cc_final: 0.8087 (t80) REVERT: B 359 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6704 (mm-30) REVERT: B 391 ASN cc_start: 0.8710 (p0) cc_final: 0.8256 (p0) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.3488 time to fit residues: 83.0483 Evaluate side-chains 142 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 10 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.123164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.091904 restraints weight = 45734.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.096865 restraints weight = 21376.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.100187 restraints weight = 13334.973| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7030 Z= 0.099 Angle : 0.453 4.734 9497 Z= 0.235 Chirality : 0.043 0.156 1035 Planarity : 0.004 0.041 1246 Dihedral : 4.204 14.176 908 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.30), residues: 849 helix: 2.49 (0.38), residues: 205 sheet: -0.86 (0.37), residues: 187 loop : -0.33 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 243 HIS 0.004 0.001 HIS B 126 PHE 0.011 0.001 PHE A 307 TYR 0.009 0.001 TYR A 82 ARG 0.001 0.000 ARG B 366 Details of bonding type rmsd hydrogen bonds : bond 0.02593 ( 228) hydrogen bonds : angle 4.38281 ( 612) covalent geometry : bond 0.00225 ( 7030) covalent geometry : angle 0.45320 ( 9497) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8451 (tt0) cc_final: 0.8205 (mt-10) REVERT: A 64 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7665 (mt-10) REVERT: A 82 TYR cc_start: 0.8470 (m-80) cc_final: 0.8153 (m-80) REVERT: A 219 ASN cc_start: 0.7974 (m-40) cc_final: 0.7222 (t0) REVERT: A 274 LEU cc_start: 0.8379 (mt) cc_final: 0.8003 (mt) REVERT: A 308 PHE cc_start: 0.8476 (m-80) cc_final: 0.8208 (m-10) REVERT: A 366 ARG cc_start: 0.8958 (mtp180) cc_final: 0.8319 (mtm-85) REVERT: B 129 ASN cc_start: 0.8763 (m-40) cc_final: 0.8460 (m-40) REVERT: B 190 TYR cc_start: 0.8308 (t80) cc_final: 0.8070 (t80) REVERT: B 359 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6697 (mm-30) REVERT: B 391 ASN cc_start: 0.8709 (p0) cc_final: 0.8240 (p0) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.3308 time to fit residues: 75.3173 Evaluate side-chains 141 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.121669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.090575 restraints weight = 46165.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.095369 restraints weight = 21601.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.098695 restraints weight = 13584.002| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7030 Z= 0.143 Angle : 0.470 4.151 9497 Z= 0.248 Chirality : 0.042 0.149 1035 Planarity : 0.004 0.041 1246 Dihedral : 4.286 14.567 908 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: 0.30 (0.30), residues: 849 helix: 2.53 (0.38), residues: 200 sheet: -0.91 (0.38), residues: 187 loop : -0.31 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 243 HIS 0.005 0.001 HIS B 126 PHE 0.011 0.001 PHE A 153 TYR 0.010 0.001 TYR A 82 ARG 0.003 0.000 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.02640 ( 228) hydrogen bonds : angle 4.46021 ( 612) covalent geometry : bond 0.00303 ( 7030) covalent geometry : angle 0.46980 ( 9497) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5811.94 seconds wall clock time: 111 minutes 10.35 seconds (6670.35 seconds total)