Starting phenix.real_space_refine on Mon Dec 30 16:28:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bah_15948/12_2024/8bah_15948.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bah_15948/12_2024/8bah_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_15948/12_2024/8bah_15948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bah_15948/12_2024/8bah_15948.map" model { file = "/net/cci-nas-00/data/ceres_data/8bah_15948/12_2024/8bah_15948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bah_15948/12_2024/8bah_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-5532/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: 6.68, per 1000 atoms: 0.49 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: 3.24 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: 1.17 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: 4.96 Time building geometry restraints manager: 3.90 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: 0.350 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: 0.240 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 31.000 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.540 ------------------------------------------------------------------------------- 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= 0.217 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 *********************** 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 : 0.920 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: 0.3974 time to fit residues: 102.8094 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 : 1.271 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 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= 0.260 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 *********************** 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 : 1.174 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: 0.7754 (m-70) cc_final: 0.6928 (m170) REVERT: A 274 LEU cc_start: 0.8210 (mt) cc_final: 0.7733 (mt) REVERT: A 308 PHE cc_start: 0.8452 (m-80) cc_final: 0.8184 (m-10) REVERT: A 366 ARG cc_start: 0.8849 (mtp180) cc_final: 0.8511 (mtm-85) REVERT: B 129 ASN cc_start: 0.8914 (m-40) cc_final: 0.8658 (m-40) REVERT: B 359 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6747 (mm-30) REVERT: B 391 ASN cc_start: 0.8641 (p0) cc_final: 0.8275 (p0) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.3443 time to fit residues: 83.6958 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 : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7030 Z= 0.259 Angle : 0.507 4.063 9497 Z= 0.273 Chirality : 0.042 0.152 1035 Planarity : 0.004 0.044 1246 Dihedral : 4.568 15.365 908 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % 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: 0.24 (0.29), residues: 849 helix: 2.03 (0.37), residues: 200 sheet: -0.89 (0.36), residues: 186 loop : -0.13 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 210 HIS 0.006 0.001 HIS C 711 PHE 0.011 0.001 PHE B 54 TYR 0.011 0.001 TYR B 179 ARG 0.003 0.000 ARG B 364 *********************** 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 : 1.244 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: 0.7672 (m-70) cc_final: 0.6859 (m170) REVERT: A 42 GLU cc_start: 0.8273 (tt0) cc_final: 0.7966 (mt-10) REVERT: A 64 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7883 (mt-10) REVERT: A 219 ASN cc_start: 0.8049 (m-40) cc_final: 0.7416 (t0) REVERT: A 274 LEU cc_start: 0.8164 (mt) cc_final: 0.7752 (mt) REVERT: A 294 MET cc_start: 0.9056 (ppp) cc_final: 0.8374 (ppp) REVERT: A 308 PHE cc_start: 0.8444 (m-80) cc_final: 0.8196 (m-10) REVERT: A 366 ARG cc_start: 0.8873 (mtp180) cc_final: 0.8449 (mtm-85) REVERT: B 128 ASN cc_start: 0.8574 (p0) cc_final: 0.8335 (p0) REVERT: B 129 ASN cc_start: 0.8875 (m-40) cc_final: 0.8566 (m-40) REVERT: B 391 ASN cc_start: 0.8732 (p0) cc_final: 0.8263 (p0) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.3547 time to fit residues: 84.6697 Evaluate side-chains 146 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 71 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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** B 100 ASN B 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 7030 Z= 0.369 Angle : 0.581 6.366 9497 Z= 0.317 Chirality : 0.043 0.154 1035 Planarity : 0.005 0.046 1246 Dihedral : 4.939 16.729 908 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.28), residues: 849 helix: 1.60 (0.36), residues: 205 sheet: -1.36 (0.37), residues: 174 loop : -0.40 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 243 HIS 0.005 0.001 HIS B 126 PHE 0.015 0.002 PHE B 54 TYR 0.010 0.002 TYR B 179 ARG 0.005 0.001 ARG B 80 *********************** 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 166 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.115 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 22 HIS cc_start: 0.7578 (m-70) cc_final: 0.6927 (m170) REVERT: A 42 GLU cc_start: 0.8356 (tt0) cc_final: 0.8083 (mt-10) REVERT: A 64 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7751 (mt-10) REVERT: A 274 LEU cc_start: 0.8329 (mt) cc_final: 0.8018 (mt) REVERT: A 294 MET cc_start: 0.9083 (ppp) cc_final: 0.8468 (ppp) REVERT: A 308 PHE cc_start: 0.8488 (m-80) cc_final: 0.8248 (m-10) REVERT: A 366 ARG cc_start: 0.8948 (mtp180) cc_final: 0.8501 (mtm-85) REVERT: B 128 ASN cc_start: 0.8768 (p0) cc_final: 0.8535 (p0) REVERT: B 129 ASN cc_start: 0.8889 (m-40) cc_final: 0.8581 (m-40) REVERT: B 391 ASN cc_start: 0.8672 (p0) cc_final: 0.8284 (p0) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.4062 time to fit residues: 96.2038 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 : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 0.5980 chunk 72 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7030 Z= 0.238 Angle : 0.507 5.063 9497 Z= 0.272 Chirality : 0.042 0.146 1035 Planarity : 0.004 0.045 1246 Dihedral : 4.688 15.560 908 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: -0.09 (0.29), residues: 849 helix: 1.97 (0.38), residues: 199 sheet: -1.26 (0.37), residues: 174 loop : -0.41 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 243 HIS 0.004 0.001 HIS B 126 PHE 0.013 0.001 PHE A 153 TYR 0.010 0.001 TYR B 179 ARG 0.002 0.000 ARG B 364 *********************** 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 169 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.179 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: A 42 GLU cc_start: 0.8272 (tt0) cc_final: 0.7979 (mt-10) REVERT: A 64 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7739 (mt-10) REVERT: A 274 LEU cc_start: 0.8283 (mt) cc_final: 0.7799 (mt) REVERT: A 308 PHE cc_start: 0.8446 (m-80) cc_final: 0.8219 (m-10) REVERT: B 82 TYR cc_start: 0.8458 (m-10) cc_final: 0.8106 (m-10) REVERT: B 128 ASN cc_start: 0.8773 (p0) cc_final: 0.8568 (p0) REVERT: B 129 ASN cc_start: 0.8875 (m-40) cc_final: 0.8550 (m-40) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.3448 time to fit residues: 82.3932 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 : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 66 optimal weight: 0.2980 chunk 37 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN A 218 GLN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7030 Z= 0.263 Angle : 0.515 4.476 9497 Z= 0.278 Chirality : 0.042 0.139 1035 Planarity : 0.004 0.044 1246 Dihedral : 4.725 16.073 908 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: -0.23 (0.29), residues: 849 helix: 1.95 (0.38), residues: 199 sheet: -1.35 (0.36), residues: 187 loop : -0.52 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 210 HIS 0.005 0.001 HIS A 22 PHE 0.012 0.002 PHE B 54 TYR 0.010 0.001 TYR B 179 ARG 0.003 0.000 ARG B 80 *********************** 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 161 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.163 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 22 HIS cc_start: 0.7587 (m170) cc_final: 0.6983 (m170) REVERT: A 42 GLU cc_start: 0.8272 (tt0) cc_final: 0.8011 (mt-10) REVERT: A 64 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7759 (mt-10) REVERT: A 142 ASP cc_start: 0.9338 (m-30) cc_final: 0.9133 (m-30) REVERT: A 219 ASN cc_start: 0.8153 (m-40) cc_final: 0.7495 (t0) REVERT: A 308 PHE cc_start: 0.8427 (m-80) cc_final: 0.8208 (m-10) REVERT: A 366 ARG cc_start: 0.8926 (mtp180) cc_final: 0.8288 (mtm-85) REVERT: B 129 ASN cc_start: 0.8874 (m-40) cc_final: 0.8540 (m-40) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.3645 time to fit residues: 82.4072 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 : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3026 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= 0.161 Angle : 0.474 4.748 9497 Z= 0.249 Chirality : 0.042 0.150 1035 Planarity : 0.004 0.043 1246 Dihedral : 4.500 14.840 908 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % 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: 0.03 (0.29), residues: 849 helix: 2.18 (0.38), residues: 200 sheet: -1.17 (0.37), residues: 168 loop : -0.41 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 108 HIS 0.002 0.001 HIS B 247 PHE 0.010 0.001 PHE B 54 TYR 0.011 0.001 TYR B 179 ARG 0.002 0.000 ARG B 364 *********************** 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 164 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.173 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: A 42 GLU cc_start: 0.8238 (tt0) cc_final: 0.7989 (mt-10) REVERT: A 64 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7732 (mt-10) REVERT: A 219 ASN cc_start: 0.8137 (m-40) cc_final: 0.7467 (t0) REVERT: A 274 LEU cc_start: 0.8344 (mt) cc_final: 0.7948 (mt) REVERT: A 308 PHE cc_start: 0.8415 (m-80) cc_final: 0.8160 (m-10) REVERT: A 366 ARG cc_start: 0.8897 (mtp180) cc_final: 0.8284 (mtm-85) REVERT: B 129 ASN cc_start: 0.8735 (m-40) cc_final: 0.8511 (m-40) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.3568 time to fit residues: 81.6959 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 : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 54 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 72 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- 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 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3143 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= 0.254 Angle : 0.505 4.176 9497 Z= 0.271 Chirality : 0.042 0.141 1035 Planarity : 0.004 0.043 1246 Dihedral : 4.614 15.390 908 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % 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: -0.11 (0.29), residues: 849 helix: 2.09 (0.38), residues: 199 sheet: -1.19 (0.37), residues: 187 loop : -0.50 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 210 HIS 0.006 0.001 HIS A 22 PHE 0.012 0.001 PHE B 13 TYR 0.010 0.001 TYR B 179 ARG 0.003 0.000 ARG B 80 *********************** 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 158 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.280 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 29 ASP cc_start: 0.7731 (t0) cc_final: 0.7530 (t0) REVERT: A 42 GLU cc_start: 0.8270 (tt0) cc_final: 0.7986 (mt-10) REVERT: A 64 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7749 (mt-10) REVERT: A 219 ASN cc_start: 0.8130 (m-40) cc_final: 0.7479 (t0) REVERT: A 298 LYS cc_start: 0.9142 (pttt) cc_final: 0.8888 (ptpp) REVERT: A 308 PHE cc_start: 0.8417 (m-80) cc_final: 0.8208 (m-10) REVERT: B 129 ASN cc_start: 0.8711 (m-40) cc_final: 0.8449 (m-40) REVERT: B 343 MET cc_start: 0.8447 (mtt) cc_final: 0.8241 (mtt) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.3626 time to fit residues: 80.7748 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 : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 22 optimal weight: 0.0470 chunk 67 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 overall best weight: 1.3680 ------------------------------------------------------------------------------- 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 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7030 Z= 0.168 Angle : 0.470 5.646 9497 Z= 0.247 Chirality : 0.043 0.152 1035 Planarity : 0.004 0.042 1246 Dihedral : 4.430 14.681 908 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.68 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: 0.04 (0.29), residues: 849 helix: 2.21 (0.38), residues: 206 sheet: -1.08 (0.38), residues: 169 loop : -0.50 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 243 HIS 0.005 0.001 HIS B 217 PHE 0.014 0.001 PHE B 91 TYR 0.012 0.001 TYR B 179 ARG 0.001 0.000 ARG B 69 *********************** 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 162 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.127 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: A 42 GLU cc_start: 0.8228 (tt0) cc_final: 0.7985 (mt-10) REVERT: A 64 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7741 (mt-10) REVERT: A 219 ASN cc_start: 0.8128 (m-40) cc_final: 0.7467 (t0) REVERT: A 308 PHE cc_start: 0.8399 (m-80) cc_final: 0.8161 (m-10) REVERT: B 129 ASN cc_start: 0.8693 (m-40) cc_final: 0.8449 (m-40) REVERT: B 190 TYR cc_start: 0.8300 (t80) cc_final: 0.8084 (t80) REVERT: B 359 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6668 (mm-30) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.3376 time to fit residues: 77.4459 Evaluate side-chains 136 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7030 Z= 0.167 Angle : 0.466 4.886 9497 Z= 0.245 Chirality : 0.042 0.152 1035 Planarity : 0.004 0.041 1246 Dihedral : 4.365 16.418 908 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % 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: 0.14 (0.30), residues: 849 helix: 2.33 (0.38), residues: 205 sheet: -1.00 (0.39), residues: 169 loop : -0.45 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 243 HIS 0.004 0.001 HIS B 126 PHE 0.014 0.001 PHE B 13 TYR 0.019 0.002 TYR A 179 ARG 0.002 0.000 ARG B 80 ********************** 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 158 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.128 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: 0.8265 (tt0) cc_final: 0.8012 (mt-10) REVERT: A 64 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7754 (mt-10) REVERT: A 219 ASN cc_start: 0.8140 (m-40) cc_final: 0.7470 (t0) REVERT: A 308 PHE cc_start: 0.8391 (m-80) cc_final: 0.8153 (m-10) REVERT: B 129 ASN cc_start: 0.8692 (m-40) cc_final: 0.8453 (m-40) REVERT: B 190 TYR cc_start: 0.8303 (t80) cc_final: 0.8080 (t80) REVERT: B 359 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6652 (mm-30) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.3552 time to fit residues: 79.6715 Evaluate side-chains 135 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 67 optimal weight: 0.0050 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 8.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- 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 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.122122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.091178 restraints weight = 45889.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.096018 restraints weight = 21480.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.099312 restraints weight = 13516.455| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 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 : 0.002 0.024 7030 Z= 0.164 Angle : 0.463 4.373 9497 Z= 0.243 Chirality : 0.042 0.151 1035 Planarity : 0.004 0.041 1246 Dihedral : 4.320 15.720 908 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.19 (0.29), residues: 849 helix: 2.42 (0.38), residues: 205 sheet: -0.95 (0.39), residues: 169 loop : -0.46 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 243 HIS 0.004 0.001 HIS B 126 PHE 0.014 0.001 PHE B 13 TYR 0.013 0.001 TYR B 179 ARG 0.002 0.000 ARG B 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3704.52 seconds wall clock time: 66 minutes 45.21 seconds (4005.21 seconds total)