Starting phenix.real_space_refine on Tue Aug 4 16:56:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cy4_46006/08_2026/9cy4_46006.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cy4_46006/08_2026/9cy4_46006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cy4_46006/08_2026/9cy4_46006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cy4_46006/08_2026/9cy4_46006.map" model { file = "/net/cci-nas-00/data/ceres_data/9cy4_46006/08_2026/9cy4_46006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cy4_46006/08_2026/9cy4_46006.cif" } resolution = 3.41 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= 0.000 sd= 0.024 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: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 3390 2.51 5 N 838 2.21 5 O 916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5183 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4186 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 20, 'TRANS': 521} Chain breaks: 5 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 912 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'PEPT-D': 1} Link IDs: {'NMTRANS': 7, 'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'MLE:plan-1': 4, 'MVA:plan-1': 1, 'BMT:plan-1': 1, 'ABA:plan-1': 1, 'SAR:plan-1': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 1.25, per 1000 atoms: 0.24 Number of scatterers: 5183 At special positions: 0 Unit cell: (61.544, 102.207, 104.405, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 916 8.00 N 838 7.00 C 3390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.04 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 100 " distance=2.03 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 Links applied TRANS " DAL L 1 " - " ALA L 11 " Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 225.2 milliseconds 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL L 1 " Number of C-beta restraints generated: 1218 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 5 sheets defined 53.7% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 26 through 51 removed outlier: 3.504A pdb=" N SER A 51 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 60 removed outlier: 3.708A pdb=" N ILE A 55 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 88 removed outlier: 4.238A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N PHE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 removed outlier: 3.541A pdb=" N ALA A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.939A pdb=" N VAL A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 200 removed outlier: 3.743A pdb=" N PHE A 199 " --> pdb=" O TYR A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.943A pdb=" N ILE A 221 " --> pdb=" O MET A 217 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 245 removed outlier: 3.607A pdb=" N ILE A 245 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 274 removed outlier: 4.155A pdb=" N ASN A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 334 Processing helix chain 'A' and resid 335 through 357 Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 381 through 400 Processing helix chain 'A' and resid 403 through 423 Processing helix chain 'A' and resid 424 through 429 removed outlier: 3.647A pdb=" N PHE A 427 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 428 " --> pdb=" O TYR A 425 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 429 " --> pdb=" O PHE A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 424 through 429' Processing helix chain 'A' and resid 530 through 552 Processing helix chain 'A' and resid 553 through 563 removed outlier: 4.142A pdb=" N ILE A 559 " --> pdb=" O HIS A 555 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL A 560 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 583 Processing helix chain 'A' and resid 585 through 597 removed outlier: 3.668A pdb=" N ILE A 589 " --> pdb=" O ILE A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 651 removed outlier: 3.824A pdb=" N SER A 629 " --> pdb=" O TYR A 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 95 removed outlier: 3.696A pdb=" N THR B 95 " --> pdb=" O PRO B 92 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436 removed outlier: 3.796A pdb=" N CYS A 474 " --> pdb=" O HIS A 520 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS A 520 " --> pdb=" O CYS A 474 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 491 through 492 removed outlier: 3.537A pdb=" N SER A 491 " --> pdb=" O TYR A 502 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 7 through 11 Processing sheet with id=AA4, first strand: chain 'B' and resid 16 through 17 removed outlier: 7.170A pdb=" N VAL B 16 " --> pdb=" O SER B 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 63 through 64 removed outlier: 6.697A pdb=" N TRP B 40 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA B 54 " --> pdb=" O MET B 38 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N MET B 38 " --> pdb=" O ALA B 54 " (cutoff:3.500A) 281 hydrogen bonds defined for protein. 822 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: 0.52 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1200 1.33 - 1.46: 1329 1.46 - 1.58: 2722 1.58 - 1.70: 1 1.70 - 1.82: 58 Bond restraints: 5310 Sorted by residual: bond pdb=" C VAL A 189 " pdb=" N PRO A 190 " ideal model delta sigma weight residual 1.334 1.395 -0.061 2.34e-02 1.83e+03 6.82e+00 bond pdb=" C ILE A 274 " pdb=" N PRO A 275 " ideal model delta sigma weight residual 1.335 1.359 -0.024 9.40e-03 1.13e+04 6.53e+00 bond pdb=" C ARG A 93 " pdb=" N PRO A 94 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.25e-02 6.40e+03 5.42e+00 bond pdb=" C ILE A 383 " pdb=" N PRO A 384 " ideal model delta sigma weight residual 1.335 1.364 -0.029 1.28e-02 6.10e+03 5.31e+00 bond pdb=" C MLE L 2 " pdb=" N MLE L 3 " ideal model delta sigma weight residual 1.329 1.360 -0.031 1.40e-02 5.10e+03 4.97e+00 ... (remaining 5305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 7005 3.23 - 6.45: 149 6.45 - 9.68: 32 9.68 - 12.91: 7 12.91 - 16.13: 3 Bond angle restraints: 7196 Sorted by residual: angle pdb=" C MLE L 2 " pdb=" N MLE L 3 " pdb=" CA MLE L 3 " ideal model delta sigma weight residual 121.70 134.36 -12.66 1.80e+00 3.09e-01 4.95e+01 angle pdb=" N BMT L 5 " pdb=" CA BMT L 5 " pdb=" CB BMT L 5 " ideal model delta sigma weight residual 111.50 123.22 -11.72 1.70e+00 3.46e-01 4.75e+01 angle pdb=" C VAL L 9 " pdb=" N MLE L 10 " pdb=" CA MLE L 10 " ideal model delta sigma weight residual 121.70 132.54 -10.84 1.80e+00 3.09e-01 3.63e+01 angle pdb=" C MLE L 3 " pdb=" N MVA L 4 " pdb=" CA MVA L 4 " ideal model delta sigma weight residual 121.70 130.83 -9.13 1.80e+00 3.09e-01 2.57e+01 angle pdb=" C MLE L 2 " pdb=" N MLE L 3 " pdb=" CN MLE L 3 " ideal model delta sigma weight residual 124.30 109.25 15.05 3.00e+00 1.11e-01 2.52e+01 ... (remaining 7191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.37: 2860 22.37 - 44.75: 186 44.75 - 67.12: 16 67.12 - 89.50: 10 89.50 - 111.87: 4 Dihedral angle restraints: 3076 sinusoidal: 1156 harmonic: 1920 Sorted by residual: dihedral pdb=" CA MVA L 4 " pdb=" C MVA L 4 " pdb=" N BMT L 5 " pdb=" CA BMT L 5 " ideal model delta harmonic sigma weight residual 180.00 68.13 111.87 0 5.00e+00 4.00e-02 5.01e+02 dihedral pdb=" CA SAR L 7 " pdb=" C SAR L 7 " pdb=" N MLE L 8 " pdb=" CA MLE L 8 " ideal model delta harmonic sigma weight residual 180.00 68.90 111.10 0 5.00e+00 4.00e-02 4.94e+02 dihedral pdb=" CA MLE L 2 " pdb=" C MLE L 2 " pdb=" N MLE L 3 " pdb=" CA MLE L 3 " ideal model delta harmonic sigma weight residual 180.00 73.44 106.56 0 5.00e+00 4.00e-02 4.54e+02 ... (remaining 3073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.212: 793 0.212 - 0.425: 8 0.425 - 0.637: 2 0.637 - 0.850: 2 0.850 - 1.062: 1 Chirality restraints: 806 Sorted by residual: chirality pdb=" CA MLE L 10 " pdb=" N MLE L 10 " pdb=" C MLE L 10 " pdb=" CB MLE L 10 " both_signs ideal model delta sigma weight residual False 2.51 1.45 1.06 2.00e-01 2.50e+01 2.82e+01 chirality pdb=" CA BMT L 5 " pdb=" N BMT L 5 " pdb=" C BMT L 5 " pdb=" CB BMT L 5 " both_signs ideal model delta sigma weight residual False 2.53 1.70 0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" CB ILE A 47 " pdb=" CA ILE A 47 " pdb=" CG1 ILE A 47 " pdb=" CG2 ILE A 47 " both_signs ideal model delta sigma weight residual False 2.64 1.97 0.67 2.00e-01 2.50e+01 1.13e+01 ... (remaining 803 not shown) Planarity restraints: 894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 369 " 0.083 5.00e-02 4.00e+02 1.24e-01 2.48e+01 pdb=" N PRO A 370 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 219 " 0.051 5.00e-02 4.00e+02 7.69e-02 9.46e+00 pdb=" N PRO A 220 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 113 " 0.050 5.00e-02 4.00e+02 7.43e-02 8.83e+00 pdb=" N PRO A 114 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 114 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 114 " 0.042 5.00e-02 4.00e+02 ... (remaining 891 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1562 2.83 - 3.35: 4502 3.35 - 3.86: 8508 3.86 - 4.38: 9445 4.38 - 4.90: 16642 Nonbonded interactions: 40659 Sorted by model distance: nonbonded pdb=" OH TYR A 338 " pdb=" O ALA A 571 " model vdw 2.310 3.040 nonbonded pdb=" O ILE A 353 " pdb=" OG1 THR A 357 " model vdw 2.338 3.040 nonbonded pdb=" O SER A 457 " pdb=" OG SER A 461 " model vdw 2.399 3.040 nonbonded pdb=" OG SER B 56 " pdb=" N SER B 57 " model vdw 2.402 3.120 nonbonded pdb=" O ASN B 34 " pdb=" OG SER B 57 " model vdw 2.435 3.040 ... (remaining 40654 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 0.730 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: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.220 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 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 : 0.006 0.097 5319 Z= 0.299 Angle : 1.216 16.132 7215 Z= 0.632 Chirality : 0.086 1.062 806 Planarity : 0.011 0.124 893 Dihedral : 15.094 111.873 1831 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.82 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.40 % 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 are not related in a simple way. whole: -3.09 (0.26), residues: 648 helix: -2.09 (0.19), residues: 334 sheet: -1.22 (0.69), residues: 63 loop : -1.96 (0.33), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 122 TYR 0.039 0.002 TYR A 640 PHE 0.034 0.002 PHE A 68 TRP 0.009 0.001 TRP B 40 HIS 0.003 0.001 HIS B 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.30 ( 5310) covalent geometry : angle 1.21527 / 0.63 ( 7196) SS BOND : bond 0.00328 / 0.19 ( 8) SS BOND : angle 1.17756 / 0.78 ( 16) hydrogen bonds : bond 0.12880 / 8.29 ( 281) hydrogen bonds : angle 7.06872 / 4.98 ( 822) link_TRANS : bond 0.01675 / 0.88 ( 1) link_TRANS : angle 2.07806 / 0.92 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: A 34 LEU cc_start: 0.7922 (tp) cc_final: 0.6998 (mm) REVERT: A 270 ILE cc_start: 0.8005 (mt) cc_final: 0.7703 (mm) REVERT: A 446 ASN cc_start: 0.7945 (t0) cc_final: 0.7532 (p0) REVERT: A 541 GLN cc_start: 0.8023 (tp40) cc_final: 0.7535 (tt0) REVERT: B 43 GLN cc_start: 0.7289 (mt0) cc_final: 0.6540 (mp10) REVERT: B 94 ASP cc_start: 0.7678 (m-30) cc_final: 0.7139 (m-30) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.0513 time to fit residues: 12.3325 Evaluate side-chains 119 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.0570 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.0770 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN A 365 GLN B 88 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.173570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.146226 restraints weight = 7932.097| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.25 r_work: 0.3630 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5319 Z= 0.153 Angle : 0.772 11.672 7215 Z= 0.368 Chirality : 0.047 0.381 806 Planarity : 0.010 0.155 893 Dihedral : 7.569 90.969 730 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.73 % Allowed : 12.75 % Favored : 84.52 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.78 % 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 are not related in a simple way. whole: -0.84 (0.30), residues: 648 helix: 0.42 (0.26), residues: 333 sheet: -1.48 (0.76), residues: 53 loop : -1.60 (0.33), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 103 TYR 0.022 0.001 TYR A 590 PHE 0.016 0.002 PHE A 30 TRP 0.005 0.001 TRP A 602 HIS 0.001 0.000 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 5310) covalent geometry : angle 0.75920 / 0.36 ( 7196) SS BOND : bond 0.00806 / 0.34 ( 8) SS BOND : angle 1.86691 / 1.51 ( 16) hydrogen bonds : bond 0.03735 / 2.57 ( 281) hydrogen bonds : angle 4.63972 / 3.27 ( 822) link_TRANS : bond 0.01423 / 0.75 ( 1) link_TRANS : angle 5.74102 / 2.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ILE cc_start: 0.7681 (mm) cc_final: 0.7387 (tp) REVERT: A 175 PHE cc_start: 0.8307 (t80) cc_final: 0.8025 (t80) REVERT: A 179 MET cc_start: 0.8391 (mmm) cc_final: 0.8161 (mtt) REVERT: A 440 MET cc_start: 0.7262 (ptm) cc_final: 0.7000 (ptm) REVERT: A 631 MET cc_start: 0.8368 (tpt) cc_final: 0.7190 (tmm) REVERT: A 640 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.7292 (t80) REVERT: B 43 GLN cc_start: 0.7424 (mt0) cc_final: 0.7047 (mp10) outliers start: 15 outliers final: 8 residues processed: 135 average time/residue: 0.0590 time to fit residues: 10.6145 Evaluate side-chains 122 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain B residue 52 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 65 optimal weight: 0.0670 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 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 = 0.4008 r_free = 0.4008 target = 0.169486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.140959 restraints weight = 7816.092| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.27 r_work: 0.3560 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5319 Z= 0.154 Angle : 0.713 11.796 7215 Z= 0.342 Chirality : 0.046 0.366 806 Planarity : 0.009 0.145 893 Dihedral : 7.300 90.133 730 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.55 % Allowed : 14.21 % Favored : 81.24 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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 are not related in a simple way. whole: 0.10 (0.32), residues: 648 helix: 1.33 (0.27), residues: 331 sheet: -1.41 (0.76), residues: 53 loop : -1.24 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 23 TYR 0.024 0.002 TYR A 590 PHE 0.015 0.001 PHE A 117 TRP 0.005 0.001 TRP A 602 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 5310) covalent geometry : angle 0.70515 / 0.34 ( 7196) SS BOND : bond 0.00608 / 0.26 ( 8) SS BOND : angle 1.57158 / 1.20 ( 16) hydrogen bonds : bond 0.03638 / 2.52 ( 281) hydrogen bonds : angle 4.40434 / 3.09 ( 822) link_TRANS : bond 0.01024 / 0.54 ( 1) link_TRANS : angle 4.03872 / 1.85 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8996 (t80) cc_final: 0.8497 (t80) REVERT: A 74 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7969 (mm-30) REVERT: A 96 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7956 (mp) REVERT: A 179 MET cc_start: 0.8587 (mmm) cc_final: 0.8374 (ttm) REVERT: A 268 PHE cc_start: 0.8820 (t80) cc_final: 0.8618 (t80) REVERT: A 359 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.8027 (p) REVERT: A 440 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.7055 (ptm) REVERT: A 640 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.7208 (t80) REVERT: B 82 THR cc_start: 0.8349 (m) cc_final: 0.8118 (p) REVERT: B 94 ASP cc_start: 0.7525 (m-30) cc_final: 0.6938 (m-30) outliers start: 25 outliers final: 16 residues processed: 133 average time/residue: 0.0565 time to fit residues: 10.0835 Evaluate side-chains 132 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 52 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 42 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.168499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.139613 restraints weight = 7754.816| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.26 r_work: 0.3547 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5319 Z= 0.143 Angle : 0.682 9.955 7215 Z= 0.330 Chirality : 0.046 0.346 806 Planarity : 0.008 0.130 893 Dihedral : 6.994 94.521 730 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.92 % Allowed : 16.03 % Favored : 79.05 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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 are not related in a simple way. whole: 0.50 (0.33), residues: 648 helix: 1.76 (0.28), residues: 331 sheet: -1.61 (0.74), residues: 53 loop : -1.11 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 42 TYR 0.023 0.002 TYR A 590 PHE 0.020 0.002 PHE A 325 TRP 0.005 0.001 TRP A 602 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 5310) covalent geometry : angle 0.67357 / 0.32 ( 7196) SS BOND : bond 0.00442 / 0.20 ( 8) SS BOND : angle 1.52072 / 1.22 ( 16) hydrogen bonds : bond 0.03511 / 2.41 ( 281) hydrogen bonds : angle 4.30208 / 3.02 ( 822) link_TRANS : bond 0.01124 / 0.59 ( 1) link_TRANS : angle 4.34716 / 1.98 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ILE cc_start: 0.8045 (mm) cc_final: 0.7767 (tp) REVERT: A 96 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8021 (mp) REVERT: A 440 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.7028 (ptm) REVERT: A 541 GLN cc_start: 0.8134 (tp40) cc_final: 0.7654 (tt0) REVERT: A 640 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.7423 (t80) REVERT: B 82 THR cc_start: 0.8451 (m) cc_final: 0.8233 (p) REVERT: B 94 ASP cc_start: 0.7399 (m-30) cc_final: 0.6959 (m-30) outliers start: 27 outliers final: 14 residues processed: 132 average time/residue: 0.0539 time to fit residues: 9.6495 Evaluate side-chains 130 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 52 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 4 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.168403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.139171 restraints weight = 7829.993| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.26 r_work: 0.3549 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5319 Z= 0.139 Angle : 0.668 9.653 7215 Z= 0.325 Chirality : 0.045 0.344 806 Planarity : 0.008 0.125 893 Dihedral : 6.922 92.826 730 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.55 % Allowed : 16.94 % Favored : 78.51 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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 are not related in a simple way. whole: 0.71 (0.33), residues: 648 helix: 1.92 (0.28), residues: 331 sheet: -1.75 (0.71), residues: 56 loop : -0.91 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 23 TYR 0.023 0.001 TYR A 590 PHE 0.015 0.002 PHE A 268 TRP 0.006 0.001 TRP B 51 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 5310) covalent geometry : angle 0.65847 / 0.32 ( 7196) SS BOND : bond 0.00625 / 0.23 ( 8) SS BOND : angle 1.68647 / 1.44 ( 16) hydrogen bonds : bond 0.03500 / 2.41 ( 281) hydrogen bonds : angle 4.28204 / 3.00 ( 822) link_TRANS : bond 0.01064 / 0.56 ( 1) link_TRANS : angle 4.37987 / 2.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 46 ILE cc_start: 0.8007 (mm) cc_final: 0.7779 (tp) REVERT: A 96 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8048 (mp) REVERT: A 440 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.7035 (ptm) REVERT: A 541 GLN cc_start: 0.8057 (tp40) cc_final: 0.7647 (tt0) REVERT: A 640 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.7432 (t80) REVERT: B 82 THR cc_start: 0.8552 (m) cc_final: 0.8329 (p) REVERT: B 94 ASP cc_start: 0.7279 (m-30) cc_final: 0.6659 (m-30) outliers start: 25 outliers final: 17 residues processed: 129 average time/residue: 0.0541 time to fit residues: 9.3133 Evaluate side-chains 130 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 502 TYR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 26 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 19 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 40 optimal weight: 0.0270 chunk 66 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.167894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.138461 restraints weight = 7770.137| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.27 r_work: 0.3537 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5319 Z= 0.144 Angle : 0.670 10.696 7215 Z= 0.327 Chirality : 0.046 0.354 806 Planarity : 0.008 0.125 893 Dihedral : 6.844 93.011 730 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.19 % Allowed : 17.49 % Favored : 78.32 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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 are not related in a simple way. whole: 0.86 (0.33), residues: 648 helix: 1.99 (0.28), residues: 332 sheet: -1.60 (0.74), residues: 56 loop : -0.79 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 23 TYR 0.022 0.001 TYR A 590 PHE 0.016 0.002 PHE A 30 TRP 0.006 0.001 TRP B 40 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 5310) covalent geometry : angle 0.66084 / 0.32 ( 7196) SS BOND : bond 0.00634 / 0.23 ( 8) SS BOND : angle 1.63751 / 1.38 ( 16) hydrogen bonds : bond 0.03527 / 2.44 ( 281) hydrogen bonds : angle 4.24038 / 2.95 ( 822) link_TRANS : bond 0.01078 / 0.57 ( 1) link_TRANS : angle 4.31225 / 1.97 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8073 (mp) REVERT: A 102 PHE cc_start: 0.8090 (t80) cc_final: 0.7826 (t80) REVERT: A 268 PHE cc_start: 0.8760 (t80) cc_final: 0.8382 (t80) REVERT: A 440 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.7013 (ptm) REVERT: A 541 GLN cc_start: 0.8105 (tp40) cc_final: 0.7674 (tt0) REVERT: A 577 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7951 (ttm) REVERT: A 640 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.7505 (t80) REVERT: B 94 ASP cc_start: 0.7368 (m-30) cc_final: 0.6651 (m-30) outliers start: 23 outliers final: 17 residues processed: 127 average time/residue: 0.0491 time to fit residues: 8.4629 Evaluate side-chains 129 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 26 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 32 optimal weight: 0.0070 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 27 optimal weight: 0.0670 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.168262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.138899 restraints weight = 7738.521| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.25 r_work: 0.3548 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5319 Z= 0.135 Angle : 0.667 9.885 7215 Z= 0.326 Chirality : 0.045 0.353 806 Planarity : 0.008 0.124 893 Dihedral : 6.727 92.162 730 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.19 % Allowed : 18.03 % Favored : 77.78 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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 are not related in a simple way. whole: 1.03 (0.34), residues: 648 helix: 2.08 (0.28), residues: 332 sheet: -1.36 (0.75), residues: 56 loop : -0.67 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 23 TYR 0.023 0.001 TYR A 590 PHE 0.026 0.002 PHE A 30 TRP 0.005 0.001 TRP A 171 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 5310) covalent geometry : angle 0.65904 / 0.32 ( 7196) SS BOND : bond 0.00550 / 0.21 ( 8) SS BOND : angle 1.39217 / 1.12 ( 16) hydrogen bonds : bond 0.03458 / 2.41 ( 281) hydrogen bonds : angle 4.21059 / 2.94 ( 822) link_TRANS : bond 0.01060 / 0.56 ( 1) link_TRANS : angle 4.39054 / 2.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8139 (mp) REVERT: A 102 PHE cc_start: 0.8215 (t80) cc_final: 0.7991 (t80) REVERT: A 268 PHE cc_start: 0.8720 (t80) cc_final: 0.8342 (t80) REVERT: A 541 GLN cc_start: 0.8244 (tp40) cc_final: 0.7722 (tt0) REVERT: A 640 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7537 (t80) REVERT: B 94 ASP cc_start: 0.7380 (m-30) cc_final: 0.6903 (m-30) REVERT: B 111 GLN cc_start: 0.8217 (mt0) cc_final: 0.7311 (pt0) outliers start: 23 outliers final: 18 residues processed: 129 average time/residue: 0.0489 time to fit residues: 8.7153 Evaluate side-chains 128 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 87 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 10 optimal weight: 7.9990 chunk 2 optimal weight: 0.0470 chunk 66 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.169250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.140219 restraints weight = 7697.369| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.24 r_work: 0.3564 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5319 Z= 0.134 Angle : 0.665 9.900 7215 Z= 0.324 Chirality : 0.045 0.362 806 Planarity : 0.008 0.124 893 Dihedral : 6.610 90.904 730 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.19 % Allowed : 17.85 % Favored : 77.96 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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 are not related in a simple way. whole: 1.08 (0.34), residues: 648 helix: 2.10 (0.28), residues: 332 sheet: -1.35 (0.74), residues: 56 loop : -0.61 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 103 TYR 0.022 0.001 TYR A 590 PHE 0.022 0.001 PHE A 30 TRP 0.004 0.001 TRP A 171 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 5310) covalent geometry : angle 0.65736 / 0.32 ( 7196) SS BOND : bond 0.00512 / 0.21 ( 8) SS BOND : angle 1.27242 / 1.00 ( 16) hydrogen bonds : bond 0.03479 / 2.44 ( 281) hydrogen bonds : angle 4.23220 / 2.95 ( 822) link_TRANS : bond 0.01047 / 0.55 ( 1) link_TRANS : angle 4.39371 / 2.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8023 (mp) REVERT: A 102 PHE cc_start: 0.8115 (t80) cc_final: 0.7851 (t80) REVERT: A 268 PHE cc_start: 0.8663 (t80) cc_final: 0.8302 (t80) REVERT: A 541 GLN cc_start: 0.8053 (tp40) cc_final: 0.7661 (tt0) REVERT: A 640 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.7468 (t80) REVERT: B 94 ASP cc_start: 0.7261 (m-30) cc_final: 0.6761 (m-30) REVERT: B 103 ARG cc_start: 0.7114 (ttt90) cc_final: 0.6876 (ttt-90) REVERT: B 111 GLN cc_start: 0.8006 (mt0) cc_final: 0.7143 (pt0) outliers start: 23 outliers final: 16 residues processed: 129 average time/residue: 0.0511 time to fit residues: 9.1934 Evaluate side-chains 120 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 26 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.166699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.137176 restraints weight = 7743.557| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.26 r_work: 0.3518 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5319 Z= 0.152 Angle : 0.703 13.606 7215 Z= 0.343 Chirality : 0.046 0.363 806 Planarity : 0.008 0.123 893 Dihedral : 6.471 90.276 730 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.64 % Allowed : 18.76 % Favored : 77.60 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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 are not related in a simple way. whole: 1.03 (0.34), residues: 648 helix: 2.04 (0.29), residues: 333 sheet: -1.27 (0.74), residues: 56 loop : -0.64 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 103 TYR 0.022 0.001 TYR A 590 PHE 0.016 0.002 PHE A 421 TRP 0.004 0.001 TRP A 602 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 5310) covalent geometry : angle 0.69542 / 0.34 ( 7196) SS BOND : bond 0.00488 / 0.20 ( 8) SS BOND : angle 1.22311 / 0.90 ( 16) hydrogen bonds : bond 0.03675 / 2.58 ( 281) hydrogen bonds : angle 4.36901 / 3.04 ( 822) link_TRANS : bond 0.01037 / 0.55 ( 1) link_TRANS : angle 4.40832 / 2.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7679 (pt) REVERT: A 96 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8036 (mp) REVERT: A 102 PHE cc_start: 0.8145 (t80) cc_final: 0.7871 (t80) REVERT: A 170 MET cc_start: 0.8817 (mmt) cc_final: 0.8451 (mmt) REVERT: A 268 PHE cc_start: 0.8664 (t80) cc_final: 0.8344 (t80) REVERT: A 577 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7932 (ttm) REVERT: A 640 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.7451 (t80) REVERT: B 94 ASP cc_start: 0.7319 (m-30) cc_final: 0.6875 (m-30) REVERT: B 103 ARG cc_start: 0.7177 (ttt90) cc_final: 0.6929 (ttt-90) REVERT: B 111 GLN cc_start: 0.8117 (mt0) cc_final: 0.7256 (pt0) outliers start: 20 outliers final: 14 residues processed: 117 average time/residue: 0.0612 time to fit residues: 9.5290 Evaluate side-chains 114 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 26 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 45 optimal weight: 0.0970 chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.169029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.139772 restraints weight = 7769.026| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.28 r_work: 0.3546 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5319 Z= 0.136 Angle : 0.666 9.365 7215 Z= 0.331 Chirality : 0.046 0.380 806 Planarity : 0.008 0.122 893 Dihedral : 6.141 89.341 730 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.10 % Allowed : 19.85 % Favored : 77.05 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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 are not related in a simple way. whole: 1.13 (0.34), residues: 648 helix: 2.15 (0.29), residues: 333 sheet: -1.22 (0.74), residues: 56 loop : -0.65 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 103 TYR 0.022 0.001 TYR A 590 PHE 0.024 0.002 PHE A 30 TRP 0.007 0.001 TRP A 171 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 5310) covalent geometry : angle 0.65769 / 0.33 ( 7196) SS BOND : bond 0.00656 / 0.23 ( 8) SS BOND : angle 1.46650 / 1.27 ( 16) hydrogen bonds : bond 0.03389 / 2.34 ( 281) hydrogen bonds : angle 4.27486 / 2.97 ( 822) link_TRANS : bond 0.01043 / 0.55 ( 1) link_TRANS : angle 4.21196 / 1.92 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8009 (mp) REVERT: A 102 PHE cc_start: 0.8123 (t80) cc_final: 0.7837 (t80) REVERT: A 268 PHE cc_start: 0.8688 (t80) cc_final: 0.8358 (t80) REVERT: A 640 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.7518 (t80) REVERT: B 94 ASP cc_start: 0.7319 (m-30) cc_final: 0.6868 (m-30) REVERT: B 103 ARG cc_start: 0.7129 (ttt90) cc_final: 0.6892 (ttt-90) REVERT: B 111 GLN cc_start: 0.8117 (mt0) cc_final: 0.7130 (pt0) outliers start: 17 outliers final: 12 residues processed: 117 average time/residue: 0.0526 time to fit residues: 8.3840 Evaluate side-chains 115 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 26 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 64 optimal weight: 0.0670 chunk 30 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.0270 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.170591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.141355 restraints weight = 7832.468| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.29 r_work: 0.3562 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5319 Z= 0.133 Angle : 0.675 9.336 7215 Z= 0.334 Chirality : 0.047 0.398 806 Planarity : 0.008 0.122 893 Dihedral : 6.004 88.371 730 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.91 % Allowed : 19.67 % Favored : 77.41 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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 are not related in a simple way. whole: 1.13 (0.34), residues: 648 helix: 2.15 (0.29), residues: 333 sheet: -1.22 (0.73), residues: 56 loop : -0.64 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 49 TYR 0.023 0.001 TYR A 590 PHE 0.042 0.002 PHE A 30 TRP 0.028 0.001 TRP B 51 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 5310) covalent geometry : angle 0.66373 / 0.33 ( 7196) SS BOND : bond 0.00574 / 0.20 ( 8) SS BOND : angle 2.07887 / 1.62 ( 16) hydrogen bonds : bond 0.03372 / 2.33 ( 281) hydrogen bonds : angle 4.28464 / 3.01 ( 822) link_TRANS : bond 0.01014 / 0.53 ( 1) link_TRANS : angle 4.11126 / 1.88 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1115.07 seconds wall clock time: 19 minutes 50.64 seconds (1190.64 seconds total)