Starting phenix.real_space_refine on Thu Jun 5 04:47:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cy4_46006/06_2025/9cy4_46006.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cy4_46006/06_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_46006/06_2025/9cy4_46006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cy4_46006/06_2025/9cy4_46006.map" model { file = "/net/cci-nas-00/data/ceres_data/9cy4_46006/06_2025/9cy4_46006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cy4_46006/06_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-5710/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: 4.38, per 1000 atoms: 0.85 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: 1.78 Conformation dependent library (CDL) restraints added in 671.0 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: 0.70 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: 2.16 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: 1.090 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.760 Find NCS groups from input model: 0.030 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.070 ------------------------------------------------------------------------------- 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 : 0.534 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: 0.1441 time to fit residues: 33.7945 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 : 0.586 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.174181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.146687 restraints weight = 7833.839| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.25 r_work: 0.3637 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 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 : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 PHE cc_start: 0.8273 (t80) cc_final: 0.7988 (t80) REVERT: A 440 MET cc_start: 0.7256 (ptm) cc_final: 0.7012 (ptm) REVERT: A 631 MET cc_start: 0.8354 (tpt) cc_final: 0.7163 (tmm) REVERT: A 640 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.7349 (t80) REVERT: B 43 GLN cc_start: 0.7426 (mt0) cc_final: 0.7068 (mp10) outliers start: 15 outliers final: 8 residues processed: 135 average time/residue: 0.1615 time to fit residues: 28.5246 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 : 0.618 ------------------------------------------------------------------------------- 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: 0.8980 chunk 14 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 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: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.168711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.140306 restraints weight = 7779.742| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.25 r_work: 0.3555 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3237 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= 0.156 Angle : 0.714 11.661 7215 Z= 0.343 Chirality : 0.046 0.363 806 Planarity : 0.009 0.147 893 Dihedral : 7.338 81.866 730 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.01 % Allowed : 14.57 % 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: 1.29 (0.27), residues: 331 sheet: -1.45 (0.76), residues: 53 loop : -1.23 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 602 HIS 0.002 0.001 HIS A 451 PHE 0.016 0.002 PHE A 117 TYR 0.024 0.001 TYR A 590 ARG 0.005 0.000 ARG B 49 Details of bonding type rmsd link_TRANS : bond 0.01049 ( 1) link_TRANS : angle 3.97255 ( 3) hydrogen bonds : bond 0.03672 ( 281) hydrogen bonds : angle 4.44284 ( 822) SS BOND : bond 0.00441 ( 8) SS BOND : angle 1.65926 ( 16) covalent geometry : bond 0.00358 ( 5310) covalent geometry : angle 0.70593 ( 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 146 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ILE cc_start: 0.8044 (mm) cc_final: 0.7777 (tp) REVERT: A 73 PHE cc_start: 0.9023 (t80) cc_final: 0.8618 (t80) REVERT: A 74 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7947 (mm-30) REVERT: A 96 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7955 (mp) REVERT: A 359 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8106 (p) REVERT: A 440 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.7025 (ptm) REVERT: A 640 TYR cc_start: 0.8535 (OUTLIER) cc_final: 0.7215 (t80) outliers start: 22 outliers final: 14 residues processed: 133 average time/residue: 0.2155 time to fit residues: 37.9057 Evaluate side-chains 131 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.573 ------------------------------------------------------------------------------- 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 233 MET 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: 2.9990 chunk 53 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 14 optimal weight: 0.4980 chunk 55 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 B 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.164575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.134805 restraints weight = 7839.945| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.27 r_work: 0.3488 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5319 Z= 0.188 Angle : 0.734 10.718 7215 Z= 0.358 Chirality : 0.047 0.355 806 Planarity : 0.009 0.132 893 Dihedral : 7.171 86.276 730 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.74 % Allowed : 16.76 % 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 (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: 0.35 (0.33), residues: 648 helix: 1.58 (0.28), residues: 331 sheet: -1.74 (0.73), residues: 56 loop : -1.06 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 602 HIS 0.003 0.001 HIS A 451 PHE 0.020 0.002 PHE A 117 TYR 0.023 0.002 TYR A 590 ARG 0.003 0.000 ARG B 71 Details of bonding type rmsd link_TRANS : bond 0.01095 ( 1) link_TRANS : angle 4.39556 ( 3) hydrogen bonds : bond 0.03888 ( 281) hydrogen bonds : angle 4.53887 ( 822) SS BOND : bond 0.00557 ( 8) SS BOND : angle 1.57088 ( 16) covalent geometry : bond 0.00445 ( 5310) covalent geometry : angle 0.72530 ( 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: 26 poor density : 117 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8064 (mp) REVERT: A 640 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.7407 (t80) REVERT: B 94 ASP cc_start: 0.7436 (m-30) cc_final: 0.6820 (m-30) outliers start: 26 outliers final: 15 residues processed: 129 average time/residue: 0.1846 time to fit residues: 32.0078 Evaluate side-chains 123 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 109 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 248 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 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 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: 10.0000 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** 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 = 0.165321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.135714 restraints weight = 7819.538| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.26 r_work: 0.3506 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3977 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= 0.162 Angle : 0.703 10.036 7215 Z= 0.342 Chirality : 0.046 0.322 806 Planarity : 0.008 0.126 893 Dihedral : 6.966 85.998 730 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.19 % Allowed : 16.94 % 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: 0.53 (0.33), residues: 648 helix: 1.69 (0.28), residues: 331 sheet: -1.77 (0.71), residues: 56 loop : -0.88 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 51 HIS 0.002 0.001 HIS A 204 PHE 0.019 0.002 PHE A 30 TYR 0.023 0.002 TYR A 590 ARG 0.001 0.000 ARG A 526 Details of bonding type rmsd link_TRANS : bond 0.01097 ( 1) link_TRANS : angle 4.44933 ( 3) hydrogen bonds : bond 0.03762 ( 281) hydrogen bonds : angle 4.46340 ( 822) SS BOND : bond 0.00711 ( 8) SS BOND : angle 1.68720 ( 16) covalent geometry : bond 0.00382 ( 5310) covalent geometry : angle 0.69392 ( 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 141 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8688 (mp0) cc_final: 0.8324 (mp0) REVERT: A 96 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8066 (mp) REVERT: A 179 MET cc_start: 0.8888 (ttm) cc_final: 0.8651 (mtt) REVERT: A 640 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.7535 (t80) REVERT: B 94 ASP cc_start: 0.7376 (m-30) cc_final: 0.6745 (m-30) outliers start: 23 outliers final: 16 residues processed: 131 average time/residue: 0.1976 time to fit residues: 34.0204 Evaluate side-chains 129 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 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 26 CYS Chi-restraints excluded: chain B residue 52 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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** ** 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 = 0.3933 r_free = 0.3933 target = 0.162750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.132633 restraints weight = 7774.649| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.29 r_work: 0.3465 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 5319 Z= 0.190 Angle : 0.732 11.240 7215 Z= 0.358 Chirality : 0.047 0.341 806 Planarity : 0.008 0.127 893 Dihedral : 6.913 87.875 730 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.37 % Allowed : 16.76 % 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: 0.56 (0.33), residues: 648 helix: 1.62 (0.28), residues: 332 sheet: -1.75 (0.72), residues: 56 loop : -0.74 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 602 HIS 0.003 0.001 HIS B 39 PHE 0.020 0.002 PHE A 117 TYR 0.025 0.002 TYR B 84 ARG 0.002 0.000 ARG A 246 Details of bonding type rmsd link_TRANS : bond 0.01108 ( 1) link_TRANS : angle 4.44409 ( 3) hydrogen bonds : bond 0.04028 ( 281) hydrogen bonds : angle 4.57997 ( 822) SS BOND : bond 0.00748 ( 8) SS BOND : angle 1.75333 ( 16) covalent geometry : bond 0.00450 ( 5310) covalent geometry : angle 0.72252 ( 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 134 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7789 (pt) REVERT: A 96 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8096 (mp) REVERT: A 179 MET cc_start: 0.8977 (ttm) cc_final: 0.8698 (ttm) REVERT: A 268 PHE cc_start: 0.8790 (t80) cc_final: 0.8439 (t80) REVERT: A 640 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.7530 (t80) REVERT: B 94 ASP cc_start: 0.7445 (m-30) cc_final: 0.7039 (m-30) REVERT: B 103 ARG cc_start: 0.7288 (ttm-80) cc_final: 0.7087 (ttm-80) outliers start: 24 outliers final: 15 residues processed: 123 average time/residue: 0.1507 time to fit residues: 24.7725 Evaluate side-chains 117 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 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 615 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 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: 2.9990 chunk 2 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 49 optimal weight: 0.0570 chunk 4 optimal weight: 0.3980 chunk 60 optimal weight: 0.0570 chunk 54 optimal weight: 9.9990 overall best weight: 0.3016 ------------------------------------------------------------------------------- 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** ** 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 = 0.3982 r_free = 0.3982 target = 0.167536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.138449 restraints weight = 7693.072| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.24 r_work: 0.3535 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5319 Z= 0.133 Angle : 0.681 8.984 7215 Z= 0.333 Chirality : 0.046 0.345 806 Planarity : 0.008 0.124 893 Dihedral : 6.490 86.421 730 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.91 % Allowed : 18.94 % Favored : 78.14 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: 0.74 (0.33), residues: 648 helix: 1.82 (0.28), residues: 332 sheet: -1.65 (0.70), residues: 56 loop : -0.73 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 171 HIS 0.003 0.001 HIS B 101 PHE 0.013 0.001 PHE A 386 TYR 0.023 0.001 TYR A 590 ARG 0.003 0.000 ARG A 246 Details of bonding type rmsd link_TRANS : bond 0.01092 ( 1) link_TRANS : angle 4.38129 ( 3) hydrogen bonds : bond 0.03599 ( 281) hydrogen bonds : angle 4.23645 ( 822) SS BOND : bond 0.00588 ( 8) SS BOND : angle 1.43174 ( 16) covalent geometry : bond 0.00295 ( 5310) covalent geometry : angle 0.67233 ( 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 127 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8635 (mp0) cc_final: 0.8338 (mp0) REVERT: A 96 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8015 (mp) REVERT: A 268 PHE cc_start: 0.8721 (t80) cc_final: 0.8359 (t80) REVERT: A 541 GLN cc_start: 0.8122 (tp40) cc_final: 0.7712 (tt0) REVERT: A 640 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.7583 (t80) REVERT: B 94 ASP cc_start: 0.7333 (m-30) cc_final: 0.6929 (m-30) outliers start: 16 outliers final: 12 residues processed: 123 average time/residue: 0.1541 time to fit residues: 24.9289 Evaluate side-chains 116 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU 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 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 615 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 26 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 0.0670 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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** ** 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 = 0.3963 r_free = 0.3963 target = 0.165870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.136217 restraints weight = 7725.670| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.26 r_work: 0.3513 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4410 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= 0.143 Angle : 0.707 10.437 7215 Z= 0.343 Chirality : 0.047 0.369 806 Planarity : 0.008 0.124 893 Dihedral : 6.381 85.917 730 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.28 % Allowed : 18.76 % 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 (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: 0.77 (0.33), residues: 648 helix: 1.81 (0.28), residues: 332 sheet: -1.61 (0.71), residues: 56 loop : -0.68 (0.38), residues: 260 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 0.020 0.002 PHE A 30 TYR 0.022 0.001 TYR A 590 ARG 0.002 0.000 ARG A 246 Details of bonding type rmsd link_TRANS : bond 0.01075 ( 1) link_TRANS : angle 4.37600 ( 3) hydrogen bonds : bond 0.03694 ( 281) hydrogen bonds : angle 4.34403 ( 822) SS BOND : bond 0.00512 ( 8) SS BOND : angle 1.30967 ( 16) covalent geometry : bond 0.00330 ( 5310) covalent geometry : angle 0.69980 ( 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 126 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8659 (mp0) cc_final: 0.8362 (mp0) REVERT: A 96 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8064 (mp) REVERT: A 268 PHE cc_start: 0.8715 (t80) cc_final: 0.8474 (t80) REVERT: A 541 GLN cc_start: 0.8095 (tp40) cc_final: 0.7679 (tt0) REVERT: A 640 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.7571 (t80) REVERT: B 94 ASP cc_start: 0.7330 (m-30) cc_final: 0.6954 (m-30) outliers start: 18 outliers final: 13 residues processed: 122 average time/residue: 0.1518 time to fit residues: 24.7206 Evaluate side-chains 115 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU 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 233 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 416 VAL 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 615 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 26 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 47 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.159839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.129286 restraints weight = 7745.882| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.28 r_work: 0.3412 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 5319 Z= 0.238 Angle : 0.786 9.470 7215 Z= 0.390 Chirality : 0.051 0.353 806 Planarity : 0.008 0.123 893 Dihedral : 6.916 83.769 730 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.28 % Allowed : 20.04 % Favored : 76.68 % 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: 0.54 (0.33), residues: 648 helix: 1.59 (0.28), residues: 330 sheet: -1.59 (0.73), residues: 56 loop : -0.75 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 602 HIS 0.004 0.001 HIS A 204 PHE 0.039 0.003 PHE A 421 TYR 0.031 0.002 TYR B 84 ARG 0.005 0.001 ARG B 103 Details of bonding type rmsd link_TRANS : bond 0.01018 ( 1) link_TRANS : angle 4.51035 ( 3) hydrogen bonds : bond 0.04350 ( 281) hydrogen bonds : angle 4.75480 ( 822) SS BOND : bond 0.00865 ( 8) SS BOND : angle 1.77460 ( 16) covalent geometry : bond 0.00570 ( 5310) covalent geometry : angle 0.77743 ( 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 117 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.7827 (pt) REVERT: A 96 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8106 (mp) REVERT: A 268 PHE cc_start: 0.8756 (t80) cc_final: 0.8549 (t80) REVERT: A 640 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.7647 (t80) REVERT: A 644 ILE cc_start: 0.8995 (mm) cc_final: 0.8744 (mt) REVERT: B 94 ASP cc_start: 0.7605 (m-30) cc_final: 0.7264 (m-30) outliers start: 18 outliers final: 14 residues processed: 111 average time/residue: 0.1566 time to fit residues: 23.3428 Evaluate side-chains 113 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU 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 464 ASN Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 615 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 26 CYS Chi-restraints excluded: chain B residue 87 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 17 optimal weight: 0.0870 chunk 41 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.164062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.134122 restraints weight = 7798.477| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.28 r_work: 0.3477 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5319 Z= 0.155 Angle : 0.722 8.916 7215 Z= 0.357 Chirality : 0.048 0.404 806 Planarity : 0.008 0.121 893 Dihedral : 6.866 79.259 730 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.73 % Allowed : 20.77 % Favored : 76.50 % 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: 0.67 (0.33), residues: 648 helix: 1.77 (0.28), residues: 332 sheet: -1.54 (0.72), residues: 56 loop : -0.83 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 602 HIS 0.003 0.001 HIS B 101 PHE 0.038 0.002 PHE A 421 TYR 0.022 0.002 TYR A 590 ARG 0.003 0.000 ARG B 103 Details of bonding type rmsd link_TRANS : bond 0.01098 ( 1) link_TRANS : angle 4.29354 ( 3) hydrogen bonds : bond 0.03805 ( 281) hydrogen bonds : angle 4.50485 ( 822) SS BOND : bond 0.00668 ( 8) SS BOND : angle 1.57781 ( 16) covalent geometry : bond 0.00362 ( 5310) covalent geometry : angle 0.71411 ( 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 120 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8760 (mp0) cc_final: 0.8451 (mp0) REVERT: A 96 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8040 (mp) REVERT: A 102 PHE cc_start: 0.8258 (t80) cc_final: 0.7993 (t80) REVERT: A 268 PHE cc_start: 0.8731 (t80) cc_final: 0.8472 (t80) REVERT: A 440 MET cc_start: 0.7343 (ptm) cc_final: 0.7099 (ptm) REVERT: A 640 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.7577 (t80) REVERT: B 94 ASP cc_start: 0.7623 (m-30) cc_final: 0.7262 (m-30) REVERT: B 111 GLN cc_start: 0.8002 (mt0) cc_final: 0.7112 (pt0) outliers start: 15 outliers final: 13 residues processed: 117 average time/residue: 0.1513 time to fit residues: 23.7339 Evaluate side-chains 117 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU 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 233 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 615 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 26 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 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 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3951 r_free = 0.3951 target = 0.164707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.134930 restraints weight = 7818.901| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.28 r_work: 0.3487 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4723 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= 0.152 Angle : 0.705 8.920 7215 Z= 0.347 Chirality : 0.048 0.407 806 Planarity : 0.008 0.122 893 Dihedral : 6.650 78.022 730 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.28 % Allowed : 20.22 % Favored : 76.50 % 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: 0.69 (0.33), residues: 648 helix: 1.81 (0.28), residues: 332 sheet: -1.69 (0.71), residues: 56 loop : -0.80 (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 A 115 PHE 0.042 0.002 PHE A 421 TYR 0.022 0.002 TYR A 590 ARG 0.002 0.000 ARG B 103 Details of bonding type rmsd link_TRANS : bond 0.01067 ( 1) link_TRANS : angle 4.23341 ( 3) hydrogen bonds : bond 0.03703 ( 281) hydrogen bonds : angle 4.48042 ( 822) SS BOND : bond 0.00613 ( 8) SS BOND : angle 1.46133 ( 16) covalent geometry : bond 0.00357 ( 5310) covalent geometry : angle 0.69755 ( 7196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2816.03 seconds wall clock time: 50 minutes 29.60 seconds (3029.60 seconds total)