Starting phenix.real_space_refine on Sat May 10 05:26:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cy4_46006/05_2025/9cy4_46006.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cy4_46006/05_2025/9cy4_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_46006/05_2025/9cy4_46006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cy4_46006/05_2025/9cy4_46006.map" model { file = "/net/cci-nas-00/data/ceres_data/9cy4_46006/05_2025/9cy4_46006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cy4_46006/05_2025/9cy4_46006.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'TYR:plan': 1, 'ARG: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 Planarities with less than four sites: {'SAR:plan-1': 1, 'ABA:plan-1': 1, 'BMT:plan-1': 1, 'MVA:plan-1': 1, 'MLE:plan-1': 4} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 3.86, per 1000 atoms: 0.74 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: 1.85 Conformation dependent library (CDL) restraints added in 638.4 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: 0.53 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: 1.53 Time building geometry restraints manager: 1.84 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 SAR L 7 " pdb=" O SAR L 7 " ideal model delta sigma weight residual 1.266 1.221 0.045 2.00e-02 2.50e+03 5.17e+00 ... (remaining 5305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 7006 3.23 - 6.45: 148 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: 2859 22.37 - 44.75: 186 44.75 - 67.12: 17 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: 1.070 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.190 Find NCS groups from input model: 0.050 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 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= 0.300 Angle : 1.214 16.132 7215 Z= 0.632 Chirality : 0.086 1.062 806 Planarity : 0.011 0.124 893 Dihedral : 15.135 111.873 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.001 TRP B 40 HIS 0.003 0.001 HIS B 61 PHE 0.034 0.002 PHE A 68 TYR 0.039 0.002 TYR A 640 ARG 0.008 0.001 ARG A 122 Details of bonding type rmsd link_TRANS : bond 0.01675 ( 1) link_TRANS : angle 2.07806 ( 3) hydrogen bonds : bond 0.12880 ( 281) hydrogen bonds : angle 7.06872 ( 822) SS BOND : bond 0.00328 ( 8) SS BOND : angle 1.17756 ( 16) covalent geometry : bond 0.00570 ( 5310) covalent geometry : angle 1.21382 ( 7196) *********************** 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 : 0.526 Fit side-chains revert: symmetry clash REVERT: A 34 LEU cc_start: 0.7922 (tp) cc_final: 0.7010 (mm) REVERT: A 270 ILE cc_start: 0.8005 (mt) cc_final: 0.7704 (mm) REVERT: A 446 ASN cc_start: 0.7945 (t0) cc_final: 0.7533 (p0) REVERT: A 541 GLN cc_start: 0.8024 (tp40) cc_final: 0.7534 (tt0) REVERT: B 43 GLN cc_start: 0.7289 (mt0) cc_final: 0.6537 (mp10) REVERT: B 94 ASP cc_start: 0.7678 (m-30) cc_final: 0.7136 (m-30) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1483 time to fit residues: 34.5722 Evaluate side-chains 118 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.0370 chunk 34 optimal weight: 0.0570 chunk 27 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4047 r_free = 0.4047 target = 0.174092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.146578 restraints weight = 7833.526| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.25 r_work: 0.3637 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5319 Z= 0.150 Angle : 0.770 11.789 7215 Z= 0.367 Chirality : 0.047 0.400 806 Planarity : 0.010 0.155 893 Dihedral : 7.552 81.538 730 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.73 % Allowed : 12.57 % Favored : 84.70 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.78 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.30), residues: 648 helix: 0.42 (0.26), residues: 333 sheet: -1.49 (0.76), residues: 53 loop : -1.60 (0.33), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 602 HIS 0.002 0.000 HIS A 115 PHE 0.019 0.002 PHE A 73 TYR 0.023 0.001 TYR A 590 ARG 0.002 0.000 ARG A 181 Details of bonding type rmsd link_TRANS : bond 0.01227 ( 1) link_TRANS : angle 5.75227 ( 3) hydrogen bonds : bond 0.03729 ( 281) hydrogen bonds : angle 4.67591 ( 822) SS BOND : bond 0.00730 ( 8) SS BOND : angle 1.85494 ( 16) covalent geometry : bond 0.00336 ( 5310) covalent geometry : angle 0.75720 ( 7196) *********************** 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 : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 PHE cc_start: 0.8273 (t80) cc_final: 0.7993 (t80) REVERT: A 440 MET cc_start: 0.7253 (ptm) cc_final: 0.6993 (ptm) REVERT: A 631 MET cc_start: 0.8347 (tpt) cc_final: 0.7171 (tmm) REVERT: A 640 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.7355 (t80) REVERT: B 43 GLN cc_start: 0.7418 (mt0) cc_final: 0.7075 (mp10) outliers start: 15 outliers final: 8 residues processed: 135 average time/residue: 0.1599 time to fit residues: 28.1658 Evaluate side-chains 124 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 6 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4003 r_free = 0.4003 target = 0.169337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.141143 restraints weight = 7801.614| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.25 r_work: 0.3571 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3141 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= 0.151 Angle : 0.708 11.629 7215 Z= 0.340 Chirality : 0.046 0.342 806 Planarity : 0.009 0.147 893 Dihedral : 7.346 82.169 730 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.64 % Allowed : 14.94 % Favored : 81.42 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.62 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.32), residues: 648 helix: 1.31 (0.27), residues: 331 sheet: -1.45 (0.76), residues: 53 loop : -1.26 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 602 HIS 0.002 0.000 HIS A 451 PHE 0.015 0.001 PHE A 117 TYR 0.024 0.001 TYR A 590 ARG 0.009 0.001 ARG B 23 Details of bonding type rmsd link_TRANS : bond 0.01025 ( 1) link_TRANS : angle 4.10004 ( 3) hydrogen bonds : bond 0.03631 ( 281) hydrogen bonds : angle 4.42843 ( 822) SS BOND : bond 0.00730 ( 8) SS BOND : angle 1.60842 ( 16) covalent geometry : bond 0.00347 ( 5310) covalent geometry : angle 0.69990 ( 7196) *********************** 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 141 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.9046 (t80) cc_final: 0.8784 (t80) REVERT: A 74 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7952 (mm-30) REVERT: A 96 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7809 (mp) REVERT: A 359 VAL cc_start: 0.8336 (OUTLIER) cc_final: 0.8020 (p) REVERT: A 440 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.7008 (ptm) REVERT: A 541 GLN cc_start: 0.8225 (tp40) cc_final: 0.7681 (tt0) REVERT: A 640 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.7210 (t80) outliers start: 20 outliers final: 13 residues processed: 130 average time/residue: 0.1489 time to fit residues: 25.6871 Evaluate side-chains 126 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 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 6 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 35 optimal weight: 0.1980 chunk 14 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3995 r_free = 0.3995 target = 0.168398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.139840 restraints weight = 7837.769| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.26 r_work: 0.3549 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3506 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= 0.145 Angle : 0.693 10.319 7215 Z= 0.336 Chirality : 0.046 0.368 806 Planarity : 0.008 0.132 893 Dihedral : 7.043 85.207 730 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.37 % Allowed : 15.48 % Favored : 80.15 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.33), residues: 648 helix: 1.70 (0.28), residues: 331 sheet: -1.62 (0.75), residues: 53 loop : -1.14 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 602 HIS 0.002 0.001 HIS B 101 PHE 0.014 0.001 PHE A 117 TYR 0.023 0.001 TYR A 590 ARG 0.001 0.000 ARG B 23 Details of bonding type rmsd link_TRANS : bond 0.01088 ( 1) link_TRANS : angle 4.31040 ( 3) hydrogen bonds : bond 0.03566 ( 281) hydrogen bonds : angle 4.33262 ( 822) SS BOND : bond 0.00538 ( 8) SS BOND : angle 1.57480 ( 16) covalent geometry : bond 0.00334 ( 5310) covalent geometry : angle 0.68411 ( 7196) *********************** 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 143 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ILE cc_start: 0.8008 (mm) cc_final: 0.7736 (tp) REVERT: A 96 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7988 (mp) REVERT: A 440 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.7063 (ptm) REVERT: A 640 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.7364 (t80) REVERT: B 82 THR cc_start: 0.8379 (m) cc_final: 0.8164 (p) REVERT: B 103 ARG cc_start: 0.7127 (ttm-80) cc_final: 0.6728 (ttt90) outliers start: 24 outliers final: 15 residues processed: 130 average time/residue: 0.1480 time to fit residues: 25.4414 Evaluate side-chains 124 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 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 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 35 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 13 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3978 r_free = 0.3978 target = 0.166598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.136986 restraints weight = 7780.514| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.27 r_work: 0.3520 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5319 Z= 0.151 Angle : 0.690 10.111 7215 Z= 0.335 Chirality : 0.046 0.345 806 Planarity : 0.008 0.125 893 Dihedral : 6.869 86.335 730 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.92 % Allowed : 16.94 % Favored : 78.14 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.33), residues: 648 helix: 1.82 (0.28), residues: 331 sheet: -1.83 (0.73), residues: 56 loop : -0.89 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 602 HIS 0.002 0.001 HIS B 39 PHE 0.018 0.002 PHE A 30 TYR 0.023 0.002 TYR A 590 ARG 0.002 0.000 ARG A 246 Details of bonding type rmsd link_TRANS : bond 0.01120 ( 1) link_TRANS : angle 4.31711 ( 3) hydrogen bonds : bond 0.03621 ( 281) hydrogen bonds : angle 4.31373 ( 822) SS BOND : bond 0.00904 ( 8) SS BOND : angle 1.58344 ( 16) covalent geometry : bond 0.00350 ( 5310) covalent geometry : angle 0.68158 ( 7196) *********************** 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 136 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ILE cc_start: 0.8030 (mm) cc_final: 0.7827 (tp) REVERT: A 96 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8044 (mp) REVERT: A 440 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.7086 (ptm) REVERT: A 640 TYR cc_start: 0.8538 (OUTLIER) cc_final: 0.7426 (t80) REVERT: B 82 THR cc_start: 0.8556 (m) cc_final: 0.8335 (p) REVERT: B 94 ASP cc_start: 0.7369 (m-30) cc_final: 0.6740 (m-30) REVERT: B 103 ARG cc_start: 0.7190 (ttm-80) cc_final: 0.6863 (ttt90) outliers start: 27 outliers final: 20 residues processed: 123 average time/residue: 0.1671 time to fit residues: 26.7012 Evaluate side-chains 125 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.165359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.136091 restraints weight = 7710.076| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.22 r_work: 0.3512 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4073 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= 0.163 Angle : 0.692 10.273 7215 Z= 0.338 Chirality : 0.046 0.349 806 Planarity : 0.008 0.126 893 Dihedral : 6.774 86.118 730 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.55 % Allowed : 16.58 % Favored : 78.87 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.33), residues: 648 helix: 1.84 (0.28), residues: 332 sheet: -1.75 (0.72), residues: 56 loop : -0.75 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 602 HIS 0.002 0.001 HIS B 101 PHE 0.016 0.002 PHE A 68 TYR 0.022 0.002 TYR A 590 ARG 0.002 0.000 ARG A 246 Details of bonding type rmsd link_TRANS : bond 0.01096 ( 1) link_TRANS : angle 4.38965 ( 3) hydrogen bonds : bond 0.03765 ( 281) hydrogen bonds : angle 4.34552 ( 822) SS BOND : bond 0.00593 ( 8) SS BOND : angle 1.73908 ( 16) covalent geometry : bond 0.00383 ( 5310) covalent geometry : angle 0.68205 ( 7196) *********************** 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 125 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8131 (mp) REVERT: A 102 PHE cc_start: 0.8212 (t80) cc_final: 0.7968 (t80) REVERT: A 170 MET cc_start: 0.8871 (mmt) cc_final: 0.8558 (mmt) REVERT: A 268 PHE cc_start: 0.8797 (t80) cc_final: 0.8418 (t80) REVERT: A 440 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.7158 (ptm) REVERT: A 640 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.7571 (t80) REVERT: B 94 ASP cc_start: 0.7288 (m-30) cc_final: 0.6619 (m-30) REVERT: B 103 ARG cc_start: 0.7419 (ttm-80) cc_final: 0.7110 (ttt90) outliers start: 25 outliers final: 18 residues processed: 113 average time/residue: 0.1465 time to fit residues: 22.2365 Evaluate side-chains 117 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU 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 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 Chi-restraints excluded: chain B residue 87 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 32 optimal weight: 0.9980 chunk 2 optimal weight: 0.0030 chunk 5 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.166488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.136846 restraints weight = 7702.295| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.25 r_work: 0.3517 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4163 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= 0.140 Angle : 0.680 9.465 7215 Z= 0.331 Chirality : 0.046 0.344 806 Planarity : 0.008 0.125 893 Dihedral : 6.518 85.752 730 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.64 % Allowed : 18.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.33), residues: 648 helix: 1.92 (0.28), residues: 332 sheet: -1.54 (0.72), residues: 56 loop : -0.72 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 602 HIS 0.002 0.001 HIS B 101 PHE 0.013 0.001 PHE A 117 TYR 0.022 0.001 TYR A 590 ARG 0.002 0.000 ARG A 246 Details of bonding type rmsd link_TRANS : bond 0.01079 ( 1) link_TRANS : angle 4.36842 ( 3) hydrogen bonds : bond 0.03633 ( 281) hydrogen bonds : angle 4.27857 ( 822) SS BOND : bond 0.00575 ( 8) SS BOND : angle 1.42590 ( 16) covalent geometry : bond 0.00322 ( 5310) covalent geometry : angle 0.67212 ( 7196) *********************** 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 123 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8084 (mp) REVERT: A 102 PHE cc_start: 0.8263 (t80) cc_final: 0.7996 (t80) REVERT: A 268 PHE cc_start: 0.8746 (t80) cc_final: 0.8367 (t80) REVERT: A 640 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.7502 (t80) REVERT: B 94 ASP cc_start: 0.7525 (m-30) cc_final: 0.6786 (m-30) outliers start: 20 outliers final: 14 residues processed: 115 average time/residue: 0.1533 time to fit residues: 23.5162 Evaluate side-chains 113 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 464 ASN 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 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 41 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.165671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.136148 restraints weight = 7736.473| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.27 r_work: 0.3501 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4298 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= 0.147 Angle : 0.691 11.878 7215 Z= 0.337 Chirality : 0.046 0.358 806 Planarity : 0.008 0.124 893 Dihedral : 6.374 85.177 730 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.46 % Allowed : 18.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.33), residues: 648 helix: 1.87 (0.28), residues: 332 sheet: -1.50 (0.72), residues: 56 loop : -0.66 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 602 HIS 0.002 0.001 HIS B 101 PHE 0.016 0.001 PHE A 117 TYR 0.022 0.001 TYR A 590 ARG 0.002 0.000 ARG A 246 Details of bonding type rmsd link_TRANS : bond 0.01074 ( 1) link_TRANS : angle 4.44779 ( 3) hydrogen bonds : bond 0.03687 ( 281) hydrogen bonds : angle 4.33211 ( 822) SS BOND : bond 0.00636 ( 8) SS BOND : angle 1.35760 ( 16) covalent geometry : bond 0.00339 ( 5310) covalent geometry : angle 0.68280 ( 7196) *********************** 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 123 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8094 (mp) REVERT: A 102 PHE cc_start: 0.8277 (t80) cc_final: 0.7936 (t80) REVERT: A 268 PHE cc_start: 0.8729 (t80) cc_final: 0.8353 (t80) REVERT: A 541 GLN cc_start: 0.8242 (tp40) cc_final: 0.7693 (tt0) REVERT: A 640 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.7528 (t80) REVERT: B 94 ASP cc_start: 0.7542 (m-30) cc_final: 0.6853 (m-30) outliers start: 19 outliers final: 14 residues processed: 115 average time/residue: 0.1540 time to fit residues: 23.6332 Evaluate side-chains 113 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 47 optimal weight: 0.5980 chunk 12 optimal weight: 0.0670 chunk 3 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 44 optimal weight: 0.0570 chunk 58 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.167790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.138778 restraints weight = 7684.373| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.26 r_work: 0.3534 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4409 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= 0.134 Angle : 0.668 9.146 7215 Z= 0.329 Chirality : 0.046 0.379 806 Planarity : 0.008 0.122 893 Dihedral : 6.280 81.903 730 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.91 % Allowed : 19.85 % Favored : 77.23 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.34), residues: 648 helix: 1.92 (0.28), residues: 333 sheet: -1.36 (0.72), residues: 56 loop : -0.66 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 171 HIS 0.002 0.000 HIS B 101 PHE 0.015 0.001 PHE A 68 TYR 0.023 0.001 TYR A 590 ARG 0.002 0.000 ARG A 246 Details of bonding type rmsd link_TRANS : bond 0.01047 ( 1) link_TRANS : angle 4.28530 ( 3) hydrogen bonds : bond 0.03396 ( 281) hydrogen bonds : angle 4.25429 ( 822) SS BOND : bond 0.00446 ( 8) SS BOND : angle 1.18481 ( 16) covalent geometry : bond 0.00303 ( 5310) covalent geometry : angle 0.66124 ( 7196) *********************** 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 120 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7998 (mp) REVERT: A 102 PHE cc_start: 0.8113 (t80) cc_final: 0.7887 (t80) REVERT: A 268 PHE cc_start: 0.8645 (t80) cc_final: 0.8356 (t80) REVERT: A 541 GLN cc_start: 0.8082 (tp40) cc_final: 0.7671 (tt0) REVERT: A 640 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.7594 (t80) REVERT: B 43 GLN cc_start: 0.7222 (mp10) cc_final: 0.6939 (mp10) REVERT: B 94 ASP cc_start: 0.7402 (m-30) cc_final: 0.6804 (m-30) REVERT: B 111 GLN cc_start: 0.8077 (mt0) cc_final: 0.7206 (pt0) outliers start: 16 outliers final: 12 residues processed: 115 average time/residue: 0.1374 time to fit residues: 21.5030 Evaluate side-chains 113 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 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 483 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 640 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 27 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 50 optimal weight: 0.0020 chunk 13 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.165168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.135493 restraints weight = 7752.693| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.30 r_work: 0.3495 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5319 Z= 0.157 Angle : 0.687 9.282 7215 Z= 0.341 Chirality : 0.047 0.410 806 Planarity : 0.008 0.122 893 Dihedral : 6.704 79.515 730 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.37 % Allowed : 20.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.33), residues: 648 helix: 1.83 (0.28), residues: 333 sheet: -1.43 (0.72), residues: 56 loop : -0.69 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 602 HIS 0.002 0.001 HIS A 204 PHE 0.020 0.002 PHE A 325 TYR 0.024 0.002 TYR A 86 ARG 0.005 0.000 ARG B 103 Details of bonding type rmsd link_TRANS : bond 0.01014 ( 1) link_TRANS : angle 4.17591 ( 3) hydrogen bonds : bond 0.03659 ( 281) hydrogen bonds : angle 4.41485 ( 822) SS BOND : bond 0.00566 ( 8) SS BOND : angle 1.64168 ( 16) covalent geometry : bond 0.00371 ( 5310) covalent geometry : angle 0.67828 ( 7196) ********************** 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 111 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8042 (mp) REVERT: A 102 PHE cc_start: 0.8202 (t80) cc_final: 0.7928 (t80) REVERT: A 268 PHE cc_start: 0.8727 (t80) cc_final: 0.8415 (t80) REVERT: A 640 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.7484 (t80) REVERT: B 43 GLN cc_start: 0.7218 (mp10) cc_final: 0.6890 (mp10) REVERT: B 94 ASP cc_start: 0.7617 (m-30) cc_final: 0.6999 (m-30) REVERT: B 111 GLN cc_start: 0.7998 (mt0) cc_final: 0.7196 (pt0) outliers start: 13 outliers final: 11 residues processed: 107 average time/residue: 0.1547 time to fit residues: 21.9021 Evaluate side-chains 108 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 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 483 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 640 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 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 39 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.166199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.136634 restraints weight = 7778.522| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.28 r_work: 0.3511 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4588 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 : 0.672 9.090 7215 Z= 0.333 Chirality : 0.046 0.406 806 Planarity : 0.008 0.122 893 Dihedral : 6.592 77.462 730 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.73 % Allowed : 20.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.33), residues: 648 helix: 1.83 (0.28), residues: 333 sheet: -1.31 (0.72), residues: 56 loop : -0.67 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 51 HIS 0.002 0.001 HIS B 101 PHE 0.020 0.002 PHE A 325 TYR 0.022 0.002 TYR A 590 ARG 0.002 0.000 ARG B 103 Details of bonding type rmsd link_TRANS : bond 0.01057 ( 1) link_TRANS : angle 4.18028 ( 3) hydrogen bonds : bond 0.03553 ( 281) hydrogen bonds : angle 4.37363 ( 822) SS BOND : bond 0.00596 ( 8) SS BOND : angle 1.47556 ( 16) covalent geometry : bond 0.00336 ( 5310) covalent geometry : angle 0.66409 ( 7196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2572.72 seconds wall clock time: 45 minutes 34.58 seconds (2734.58 seconds total)