Starting phenix.real_space_refine on Sat Aug 23 17:07:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bah_15948/08_2025/8bah_15948.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bah_15948/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8bah_15948/08_2025/8bah_15948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bah_15948/08_2025/8bah_15948.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bah_15948/08_2025/8bah_15948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bah_15948/08_2025/8bah_15948.map" } resolution = 4.13 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.98, per 1000 atoms: 0.22 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: 0.85 Conformation dependent library (CDL) restraints added in 422.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.24 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: 2.85 Time building geometry restraints manager: 1.25 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 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: 0.480 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: 0.080 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.300 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.200 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG B 380 TYR 0.007 0.001 TYR A 82 PHE 0.012 0.001 PHE C 688 TRP 0.004 0.001 TRP A 210 HIS 0.003 0.000 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 7030) covalent geometry : angle 0.53713 ( 9497) hydrogen bonds : bond 0.18417 ( 228) hydrogen bonds : angle 7.65902 ( 612) *********************** 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 : 0.234 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: symmetry clash REVERT: A 22 HIS cc_start: 0.7535 (m-70) cc_final: 0.6873 (m170) 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: 0.8181 (m-10) REVERT: A 366 ARG cc_start: 0.8728 (mtp180) cc_final: 0.8502 (mtm-85) REVERT: B 359 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6768 (mm-30) REVERT: B 391 ASN cc_start: 0.8566 (p0) cc_final: 0.8312 (p0) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1731 time to fit residues: 44.8240 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 : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.3980 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.124039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.092724 restraints weight = 45669.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.097567 restraints weight = 21776.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.100893 restraints weight = 13696.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.102855 restraints weight = 10145.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.104491 restraints weight = 8441.895| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7030 Z= 0.163 Angle : 0.502 3.969 9497 Z= 0.274 Chirality : 0.043 0.165 1035 Planarity : 0.004 0.040 1246 Dihedral : 4.388 15.504 908 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.29), residues: 849 helix: 1.99 (0.37), residues: 206 sheet: -0.59 (0.37), residues: 180 loop : 0.10 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 155 TYR 0.011 0.001 TYR B 179 PHE 0.012 0.001 PHE C 688 TRP 0.006 0.001 TRP A 210 HIS 0.003 0.001 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7030) covalent geometry : angle 0.50205 ( 9497) hydrogen bonds : bond 0.04325 ( 228) hydrogen bonds : angle 5.64501 ( 612) *********************** 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 : 0.263 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: A 22 HIS cc_start: 0.7915 (m-70) cc_final: 0.7042 (m170) REVERT: A 294 MET cc_start: 0.9171 (ppp) cc_final: 0.8346 (ppp) REVERT: A 308 PHE cc_start: 0.8486 (m-80) cc_final: 0.8180 (m-10) REVERT: A 366 ARG cc_start: 0.8895 (mtp180) cc_final: 0.8528 (mtm-85) REVERT: B 42 GLU cc_start: 0.9005 (tt0) cc_final: 0.8778 (tt0) REVERT: B 129 ASN cc_start: 0.8975 (m-40) cc_final: 0.8622 (m-40) REVERT: B 359 GLU cc_start: 0.7381 (mm-30) cc_final: 0.6917 (mm-30) REVERT: B 391 ASN cc_start: 0.8501 (p0) cc_final: 0.8164 (p0) REVERT: C 693 TYR cc_start: 0.7377 (p90) cc_final: 0.7106 (p90) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1483 time to fit residues: 35.9532 Evaluate side-chains 144 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 35 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 247 HIS ** 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 = 0.3866 r_free = 0.3866 target = 0.123570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.091658 restraints weight = 46251.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.096557 restraints weight = 22124.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.099906 restraints weight = 14034.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.102201 restraints weight = 10462.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.103232 restraints weight = 8604.404| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7030 Z= 0.135 Angle : 0.474 4.055 9497 Z= 0.253 Chirality : 0.042 0.154 1035 Planarity : 0.004 0.043 1246 Dihedral : 4.361 15.019 908 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.29), residues: 849 helix: 2.28 (0.38), residues: 200 sheet: -0.64 (0.36), residues: 186 loop : -0.04 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 364 TYR 0.011 0.001 TYR B 179 PHE 0.014 0.001 PHE A 37 TRP 0.005 0.001 TRP B 108 HIS 0.008 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7030) covalent geometry : angle 0.47422 ( 9497) hydrogen bonds : bond 0.03267 ( 228) hydrogen bonds : angle 5.07993 ( 612) *********************** 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 177 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.401 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: A 22 HIS cc_start: 0.7848 (m-70) cc_final: 0.6979 (m170) REVERT: A 42 GLU cc_start: 0.8554 (tt0) cc_final: 0.8182 (mt-10) REVERT: A 64 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7751 (mt-10) REVERT: A 142 ASP cc_start: 0.9324 (m-30) cc_final: 0.9089 (m-30) REVERT: A 308 PHE cc_start: 0.8483 (m-80) cc_final: 0.8164 (m-10) REVERT: A 366 ARG cc_start: 0.8930 (mtp180) cc_final: 0.8495 (mtm-85) REVERT: B 128 ASN cc_start: 0.8402 (p0) cc_final: 0.8197 (p0) REVERT: B 129 ASN cc_start: 0.8896 (m-40) cc_final: 0.8602 (m-40) REVERT: B 359 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6863 (mm-30) REVERT: B 391 ASN cc_start: 0.8671 (p0) cc_final: 0.8145 (p0) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1442 time to fit residues: 36.3215 Evaluate side-chains 152 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 18 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 247 HIS ** 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 = 0.3865 r_free = 0.3865 target = 0.123771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.092306 restraints weight = 45600.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.097116 restraints weight = 21672.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.100382 restraints weight = 13668.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.102675 restraints weight = 10181.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.104278 restraints weight = 8346.666| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7030 Z= 0.132 Angle : 0.469 5.329 9497 Z= 0.248 Chirality : 0.042 0.157 1035 Planarity : 0.004 0.042 1246 Dihedral : 4.273 14.240 908 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.29), residues: 849 helix: 2.33 (0.38), residues: 200 sheet: -0.70 (0.36), residues: 186 loop : -0.09 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 364 TYR 0.010 0.001 TYR B 179 PHE 0.009 0.001 PHE B 54 TRP 0.008 0.001 TRP B 243 HIS 0.007 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7030) covalent geometry : angle 0.46894 ( 9497) hydrogen bonds : bond 0.03032 ( 228) hydrogen bonds : angle 4.84696 ( 612) *********************** 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 171 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.295 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 42 GLU cc_start: 0.8548 (tt0) cc_final: 0.8293 (mt-10) REVERT: A 64 GLU cc_start: 0.8407 (mm-30) cc_final: 0.7776 (mt-10) REVERT: A 308 PHE cc_start: 0.8481 (m-80) cc_final: 0.8175 (m-10) REVERT: A 366 ARG cc_start: 0.8927 (mtp180) cc_final: 0.8554 (mtm-85) REVERT: B 128 ASN cc_start: 0.8461 (p0) cc_final: 0.8194 (p0) REVERT: B 129 ASN cc_start: 0.8847 (m-40) cc_final: 0.8434 (m-40) REVERT: B 215 VAL cc_start: 0.9091 (p) cc_final: 0.8867 (m) REVERT: B 359 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6830 (mm-30) REVERT: B 391 ASN cc_start: 0.8641 (p0) cc_final: 0.8251 (p0) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1368 time to fit residues: 33.4204 Evaluate side-chains 151 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 69 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 ASN ** B 247 HIS ** 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 = 0.3864 r_free = 0.3864 target = 0.123733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.092171 restraints weight = 46289.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.097092 restraints weight = 21733.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.100427 restraints weight = 13636.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.102737 restraints weight = 10098.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.104342 restraints weight = 8259.974| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7030 Z= 0.120 Angle : 0.458 4.299 9497 Z= 0.241 Chirality : 0.042 0.154 1035 Planarity : 0.004 0.042 1246 Dihedral : 4.243 14.870 908 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.29), residues: 849 helix: 2.35 (0.38), residues: 200 sheet: -0.60 (0.37), residues: 186 loop : -0.09 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 364 TYR 0.010 0.001 TYR B 179 PHE 0.027 0.001 PHE A 261 TRP 0.005 0.001 TRP B 243 HIS 0.005 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7030) covalent geometry : angle 0.45795 ( 9497) hydrogen bonds : bond 0.02826 ( 228) hydrogen bonds : angle 4.70075 ( 612) *********************** 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 173 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.320 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 22 HIS cc_start: 0.7773 (m170) cc_final: 0.6940 (m170) REVERT: A 42 GLU cc_start: 0.8538 (tt0) cc_final: 0.8269 (mt-10) REVERT: A 64 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7758 (mt-10) REVERT: A 142 ASP cc_start: 0.9307 (m-30) cc_final: 0.9059 (m-30) REVERT: A 308 PHE cc_start: 0.8471 (m-80) cc_final: 0.8188 (m-10) REVERT: A 366 ARG cc_start: 0.8949 (mtp180) cc_final: 0.8301 (mtm-85) REVERT: B 129 ASN cc_start: 0.8853 (m-40) cc_final: 0.8484 (m-40) REVERT: B 215 VAL cc_start: 0.9076 (p) cc_final: 0.8822 (m) REVERT: B 359 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6844 (mm-30) REVERT: B 391 ASN cc_start: 0.8764 (p0) cc_final: 0.8185 (p0) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1424 time to fit residues: 34.7365 Evaluate side-chains 151 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN ** B 247 HIS ** 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 = 0.3823 r_free = 0.3823 target = 0.121068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.090430 restraints weight = 46032.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.095173 restraints weight = 21852.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.098352 restraints weight = 13773.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.100568 restraints weight = 10226.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.102083 restraints weight = 8368.989| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7030 Z= 0.221 Angle : 0.522 4.202 9497 Z= 0.282 Chirality : 0.042 0.145 1035 Planarity : 0.004 0.043 1246 Dihedral : 4.553 15.942 908 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.29), residues: 849 helix: 2.13 (0.38), residues: 200 sheet: -0.86 (0.37), residues: 187 loop : -0.26 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 364 TYR 0.009 0.001 TYR B 179 PHE 0.016 0.001 PHE A 261 TRP 0.010 0.001 TRP A 210 HIS 0.008 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 7030) covalent geometry : angle 0.52160 ( 9497) hydrogen bonds : bond 0.03037 ( 228) hydrogen bonds : angle 4.92441 ( 612) *********************** 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 163 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.406 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: 0.8493 (tt0) cc_final: 0.8209 (mt-10) REVERT: A 64 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7700 (mt-10) REVERT: A 142 ASP cc_start: 0.9302 (m-30) cc_final: 0.9098 (m-30) REVERT: A 294 MET cc_start: 0.9127 (ppp) cc_final: 0.8441 (ppp) REVERT: A 298 LYS cc_start: 0.9212 (pttt) cc_final: 0.8934 (ptpp) REVERT: A 308 PHE cc_start: 0.8515 (m-80) cc_final: 0.8215 (m-10) REVERT: A 366 ARG cc_start: 0.8974 (mtp180) cc_final: 0.8319 (mtm-85) REVERT: B 128 ASN cc_start: 0.8741 (p0) cc_final: 0.8532 (p0) REVERT: B 129 ASN cc_start: 0.8974 (m-40) cc_final: 0.8570 (m110) REVERT: B 391 ASN cc_start: 0.8658 (p0) cc_final: 0.8280 (p0) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1657 time to fit residues: 38.0753 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 : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 48 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 HIS ** 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 = 0.3832 r_free = 0.3832 target = 0.121416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.090394 restraints weight = 46082.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.095141 restraints weight = 21872.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.098410 restraints weight = 13849.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.100698 restraints weight = 10276.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.102266 restraints weight = 8405.505| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7030 Z= 0.176 Angle : 0.495 4.443 9497 Z= 0.265 Chirality : 0.042 0.145 1035 Planarity : 0.004 0.043 1246 Dihedral : 4.502 15.338 908 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.29), residues: 849 helix: 2.09 (0.38), residues: 206 sheet: -0.99 (0.38), residues: 169 loop : -0.33 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 364 TYR 0.009 0.001 TYR B 179 PHE 0.014 0.001 PHE A 261 TRP 0.006 0.001 TRP A 210 HIS 0.006 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7030) covalent geometry : angle 0.49457 ( 9497) hydrogen bonds : bond 0.02874 ( 228) hydrogen bonds : angle 4.82021 ( 612) *********************** 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 169 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.414 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: 0.8498 (tt0) cc_final: 0.8231 (mt-10) REVERT: A 64 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7633 (mt-10) REVERT: A 306 GLN cc_start: 0.7633 (mp10) cc_final: 0.7148 (mp10) REVERT: A 308 PHE cc_start: 0.8503 (m-80) cc_final: 0.8232 (m-10) REVERT: A 366 ARG cc_start: 0.8974 (mtp180) cc_final: 0.8329 (mtm-85) REVERT: B 129 ASN cc_start: 0.8936 (m-40) cc_final: 0.8505 (m110) REVERT: B 391 ASN cc_start: 0.8798 (p0) cc_final: 0.8210 (p0) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1647 time to fit residues: 39.1602 Evaluate side-chains 148 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 HIS ** 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 = 0.3820 r_free = 0.3820 target = 0.120692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.089459 restraints weight = 46242.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.094208 restraints weight = 22172.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.097465 restraints weight = 14100.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.099681 restraints weight = 10527.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.100712 restraints weight = 8658.445| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7030 Z= 0.188 Angle : 0.507 4.633 9497 Z= 0.273 Chirality : 0.042 0.143 1035 Planarity : 0.004 0.043 1246 Dihedral : 4.543 15.434 908 Min Nonbonded Distance : 1.850 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.29), residues: 849 helix: 2.05 (0.38), residues: 206 sheet: -0.98 (0.38), residues: 187 loop : -0.39 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 364 TYR 0.012 0.001 TYR B 179 PHE 0.012 0.002 PHE B 13 TRP 0.007 0.001 TRP A 210 HIS 0.006 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 7030) covalent geometry : angle 0.50685 ( 9497) hydrogen bonds : bond 0.02888 ( 228) hydrogen bonds : angle 4.79466 ( 612) *********************** 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 165 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.463 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 42 GLU cc_start: 0.8454 (tt0) cc_final: 0.8226 (mt-10) REVERT: A 64 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7652 (mt-10) REVERT: A 142 ASP cc_start: 0.9340 (m-30) cc_final: 0.9092 (m-30) REVERT: A 308 PHE cc_start: 0.8492 (m-80) cc_final: 0.8235 (m-10) REVERT: A 366 ARG cc_start: 0.8982 (mtp180) cc_final: 0.8321 (mtm-85) REVERT: B 129 ASN cc_start: 0.8783 (m-40) cc_final: 0.8433 (m-40) REVERT: B 391 ASN cc_start: 0.8672 (p0) cc_final: 0.8241 (p0) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1733 time to fit residues: 40.2044 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 : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 247 HIS ** 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 = 0.3835 r_free = 0.3835 target = 0.121540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.090296 restraints weight = 46317.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.095151 restraints weight = 22057.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.098425 restraints weight = 13899.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.100640 restraints weight = 10347.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.101673 restraints weight = 8501.305| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7030 Z= 0.145 Angle : 0.482 4.397 9497 Z= 0.256 Chirality : 0.043 0.150 1035 Planarity : 0.004 0.043 1246 Dihedral : 4.446 15.121 908 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.30), residues: 849 helix: 2.19 (0.38), residues: 206 sheet: -0.89 (0.39), residues: 182 loop : -0.35 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 364 TYR 0.008 0.001 TYR A 82 PHE 0.013 0.001 PHE B 13 TRP 0.005 0.001 TRP A 108 HIS 0.005 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7030) covalent geometry : angle 0.48212 ( 9497) hydrogen bonds : bond 0.02803 ( 228) hydrogen bonds : angle 4.65618 ( 612) *********************** 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 : 0.406 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 42 GLU cc_start: 0.8456 (tt0) cc_final: 0.8214 (mt-10) REVERT: A 64 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7657 (mt-10) REVERT: A 219 ASN cc_start: 0.7979 (m-40) cc_final: 0.7260 (t0) REVERT: A 298 LYS cc_start: 0.9199 (pttt) cc_final: 0.8908 (ptpp) REVERT: A 308 PHE cc_start: 0.8482 (m-80) cc_final: 0.8216 (m-10) REVERT: A 366 ARG cc_start: 0.8999 (mtp180) cc_final: 0.8339 (mtm-85) REVERT: B 129 ASN cc_start: 0.8923 (m-40) cc_final: 0.8474 (m110) REVERT: B 391 ASN cc_start: 0.8705 (p0) cc_final: 0.8260 (p0) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1602 time to fit residues: 37.9203 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 : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 0.0050 chunk 48 optimal weight: 7.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 HIS ** 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 = 0.3833 r_free = 0.3833 target = 0.121502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.089962 restraints weight = 46172.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.094828 restraints weight = 21694.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.098175 restraints weight = 13702.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.100466 restraints weight = 10177.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.101831 restraints weight = 8340.157| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3137 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= 0.134 Angle : 0.470 4.101 9497 Z= 0.248 Chirality : 0.042 0.148 1035 Planarity : 0.004 0.042 1246 Dihedral : 4.357 14.614 908 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.30), residues: 849 helix: 2.34 (0.38), residues: 206 sheet: -0.85 (0.38), residues: 187 loop : -0.37 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 364 TYR 0.008 0.001 TYR A 82 PHE 0.013 0.001 PHE A 307 TRP 0.006 0.001 TRP A 108 HIS 0.004 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7030) covalent geometry : angle 0.46974 ( 9497) hydrogen bonds : bond 0.02690 ( 228) hydrogen bonds : angle 4.54816 ( 612) ********************** 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 165 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.409 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 42 GLU cc_start: 0.8490 (tt0) cc_final: 0.8244 (mt-10) REVERT: A 64 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7654 (mt-10) REVERT: A 142 ASP cc_start: 0.9357 (m-30) cc_final: 0.9150 (m-30) REVERT: A 219 ASN cc_start: 0.7957 (m-40) cc_final: 0.7223 (t0) REVERT: A 298 LYS cc_start: 0.9202 (pttt) cc_final: 0.8924 (ptpp) REVERT: A 308 PHE cc_start: 0.8484 (m-80) cc_final: 0.8202 (m-10) REVERT: A 366 ARG cc_start: 0.8944 (mtp180) cc_final: 0.8305 (mtm-85) REVERT: B 129 ASN cc_start: 0.8748 (m-40) cc_final: 0.8377 (m110) REVERT: B 391 ASN cc_start: 0.8702 (p0) cc_final: 0.8255 (p0) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1627 time to fit residues: 38.1701 Evaluate side-chains 144 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** B 247 HIS ** 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 = 0.3810 r_free = 0.3810 target = 0.119909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.088458 restraints weight = 47117.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.093155 restraints weight = 22719.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.096374 restraints weight = 14487.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098530 restraints weight = 10864.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.100064 restraints weight = 8982.268| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7030 Z= 0.229 Angle : 0.537 4.385 9497 Z= 0.291 Chirality : 0.042 0.157 1035 Planarity : 0.005 0.043 1246 Dihedral : 4.691 15.456 908 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.29), residues: 849 helix: 2.15 (0.38), residues: 206 sheet: -1.15 (0.38), residues: 187 loop : -0.54 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 80 TYR 0.010 0.002 TYR A 82 PHE 0.014 0.002 PHE B 237 TRP 0.010 0.001 TRP A 210 HIS 0.008 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 7030) covalent geometry : angle 0.53674 ( 9497) hydrogen bonds : bond 0.03051 ( 228) hydrogen bonds : angle 4.88444 ( 612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2513.10 seconds wall clock time: 43 minutes 37.83 seconds (2617.83 seconds total)