Starting phenix.real_space_refine on Wed Sep 17 06:59:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mx5_48710/09_2025/9mx5_48710.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mx5_48710/09_2025/9mx5_48710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mx5_48710/09_2025/9mx5_48710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mx5_48710/09_2025/9mx5_48710.map" model { file = "/net/cci-nas-00/data/ceres_data/9mx5_48710/09_2025/9mx5_48710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mx5_48710/09_2025/9mx5_48710.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 54 5.49 5 Mg 1 5.21 5 S 25 5.16 5 C 3858 2.51 5 N 1133 2.21 5 O 1388 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6463 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5292 Classifications: {'peptide': 652} Link IDs: {'PTRANS': 26, 'TRANS': 625} Chain: "B" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 566 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna3p_pur': 12, 'rna3p_pyr': 15} Link IDs: {'rna3p': 26} Chain: "C" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 573 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna3p_pur': 15, 'rna3p_pyr': 12} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.53, per 1000 atoms: 0.24 Number of scatterers: 6463 At special positions: 0 Unit cell: (92.432, 92.432, 112.488, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 25 16.00 P 54 15.00 Al 1 13.00 Mg 1 11.99 F 3 9.00 O 1388 8.00 N 1133 7.00 C 3858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 285.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1262 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 3 sheets defined 53.2% alpha, 10.3% beta 27 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 12 through 25 removed outlier: 3.646A pdb=" N LYS A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 48 removed outlier: 3.504A pdb=" N LEU A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 52 removed outlier: 3.766A pdb=" N ILE A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 52' Processing helix chain 'A' and resid 69 through 84 Processing helix chain 'A' and resid 101 through 112 removed outlier: 3.546A pdb=" N HIS A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 151 through 162 removed outlier: 3.884A pdb=" N ASN A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 168 removed outlier: 3.520A pdb=" N ASP A 167 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG A 168 " --> pdb=" O GLN A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 164 through 168' Processing helix chain 'A' and resid 187 through 200 Processing helix chain 'A' and resid 234 through 258 Processing helix chain 'A' and resid 262 through 283 removed outlier: 3.774A pdb=" N LEU A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 303 Processing helix chain 'A' and resid 307 through 331 removed outlier: 3.646A pdb=" N ASN A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 331 " --> pdb=" O VAL A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 344 through 364 removed outlier: 4.491A pdb=" N ASN A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 394 removed outlier: 3.517A pdb=" N ALA A 380 " --> pdb=" O ARG A 376 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 468 through 479 removed outlier: 4.591A pdb=" N ALA A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 516 removed outlier: 3.553A pdb=" N ARG A 514 " --> pdb=" O LYS A 510 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 removed outlier: 3.652A pdb=" N PHE A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 552 through 564 removed outlier: 3.503A pdb=" N LEU A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 633 Processing helix chain 'A' and resid 645 through 652 Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 91 removed outlier: 6.250A pdb=" N GLY A 89 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N THR A 118 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N TYR A 91 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR A 63 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N MET A 117 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N PHE A 65 " --> pdb=" O MET A 117 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ARG A 62 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A 139 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N PHE A 64 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE A 141 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU A 66 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 170 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR A 27 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 173 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE A 28 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 222 through 228 removed outlier: 5.964A pdb=" N LYS A 222 " --> pdb=" O TYR A 486 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE A 488 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE A 224 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL A 490 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL A 226 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET A 489 " --> pdb=" O ARG A 462 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE A 371 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP A 404 " --> pdb=" O VAL A 443 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 575 through 582 removed outlier: 3.528A pdb=" N GLN A 581 " --> pdb=" O MET A 589 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A 589 " --> pdb=" O GLN A 581 " (cutoff:3.500A) 249 hydrogen bonds defined for protein. 738 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 130 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1859 1.34 - 1.46: 1266 1.46 - 1.58: 3410 1.58 - 1.70: 110 1.70 - 1.81: 38 Bond restraints: 6683 Sorted by residual: bond pdb=" CG LEU A 299 " pdb=" CD2 LEU A 299 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.81e+00 bond pdb=" C4 ADP A 702 " pdb=" C5 ADP A 702 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.33e+00 bond pdb=" CB VAL A 73 " pdb=" CG1 VAL A 73 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.03e+00 bond pdb=" CB GLN A 581 " pdb=" CG GLN A 581 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.31e-01 bond pdb=" CA ILE A 598 " pdb=" CB ILE A 598 " ideal model delta sigma weight residual 1.545 1.531 0.013 1.45e-02 4.76e+03 8.28e-01 ... (remaining 6678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 9130 1.78 - 3.56: 105 3.56 - 5.35: 18 5.35 - 7.13: 7 7.13 - 8.91: 3 Bond angle restraints: 9263 Sorted by residual: angle pdb=" CB MET A 632 " pdb=" CG MET A 632 " pdb=" SD MET A 632 " ideal model delta sigma weight residual 112.70 121.61 -8.91 3.00e+00 1.11e-01 8.82e+00 angle pdb=" CB MET A 589 " pdb=" CG MET A 589 " pdb=" SD MET A 589 " ideal model delta sigma weight residual 112.70 121.56 -8.86 3.00e+00 1.11e-01 8.73e+00 angle pdb=" CB MET A 157 " pdb=" CG MET A 157 " pdb=" SD MET A 157 " ideal model delta sigma weight residual 112.70 120.91 -8.21 3.00e+00 1.11e-01 7.49e+00 angle pdb=" CA GLN A 581 " pdb=" CB GLN A 581 " pdb=" CG GLN A 581 " ideal model delta sigma weight residual 114.10 118.97 -4.87 2.00e+00 2.50e-01 5.93e+00 angle pdb=" CA LEU A 316 " pdb=" CB LEU A 316 " pdb=" CG LEU A 316 " ideal model delta sigma weight residual 116.30 123.39 -7.09 3.50e+00 8.16e-02 4.11e+00 ... (remaining 9258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 3545 17.73 - 35.46: 446 35.46 - 53.19: 133 53.19 - 70.92: 59 70.92 - 88.64: 19 Dihedral angle restraints: 4202 sinusoidal: 2272 harmonic: 1930 Sorted by residual: dihedral pdb=" CA ARG A 603 " pdb=" C ARG A 603 " pdb=" N GLU A 604 " pdb=" CA GLU A 604 " ideal model delta harmonic sigma weight residual -180.00 -163.39 -16.61 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CB GLU A 309 " pdb=" CG GLU A 309 " pdb=" CD GLU A 309 " pdb=" OE1 GLU A 309 " ideal model delta sinusoidal sigma weight residual 0.00 88.64 -88.64 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CG ARG A 170 " pdb=" CD ARG A 170 " pdb=" NE ARG A 170 " pdb=" CZ ARG A 170 " ideal model delta sinusoidal sigma weight residual 90.00 133.83 -43.83 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 4199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 775 0.032 - 0.063: 210 0.063 - 0.095: 61 0.095 - 0.126: 35 0.126 - 0.158: 3 Chirality restraints: 1084 Sorted by residual: chirality pdb=" CA LEU A 299 " pdb=" N LEU A 299 " pdb=" C LEU A 299 " pdb=" CB LEU A 299 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CB ILE A 454 " pdb=" CA ILE A 454 " pdb=" CG1 ILE A 454 " pdb=" CG2 ILE A 454 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA ILE A 28 " pdb=" N ILE A 28 " pdb=" C ILE A 28 " pdb=" CB ILE A 28 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 1081 not shown) Planarity restraints: 992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 151 " -0.030 5.00e-02 4.00e+02 4.61e-02 3.41e+00 pdb=" N PRO A 152 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 152 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 152 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 184 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO A 185 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 185 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 185 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A B 24 " -0.016 2.00e-02 2.50e+03 7.27e-03 1.45e+00 pdb=" N9 A B 24 " 0.017 2.00e-02 2.50e+03 pdb=" C8 A B 24 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B 24 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A B 24 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A B 24 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A B 24 " -0.004 2.00e-02 2.50e+03 pdb=" N1 A B 24 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A B 24 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A B 24 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A B 24 " 0.001 2.00e-02 2.50e+03 ... (remaining 989 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 291 2.72 - 3.26: 6384 3.26 - 3.81: 10639 3.81 - 4.35: 12579 4.35 - 4.90: 19658 Nonbonded interactions: 49551 Sorted by model distance: nonbonded pdb=" F1 AF3 A 701 " pdb=" O3B ADP A 702 " model vdw 2.169 2.990 nonbonded pdb=" OG SER A 412 " pdb=" OG SER A 414 " model vdw 2.278 3.040 nonbonded pdb=" O SER A 600 " pdb=" NH1 ARG A 603 " model vdw 2.283 3.120 nonbonded pdb=" N ASP A 544 " pdb=" OD1 ASP A 544 " model vdw 2.317 3.120 nonbonded pdb=" OG SER A 252 " pdb=" NZ LYS A 270 " model vdw 2.340 3.120 ... (remaining 49546 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.640 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6683 Z= 0.147 Angle : 0.555 8.910 9263 Z= 0.277 Chirality : 0.037 0.158 1084 Planarity : 0.004 0.046 992 Dihedral : 18.208 88.644 2940 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.15 % Favored : 95.69 % Rotamer: Outliers : 1.32 % Allowed : 21.16 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.32), residues: 650 helix: 3.26 (0.28), residues: 304 sheet: 1.27 (0.57), residues: 85 loop : -1.02 (0.32), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 547 TYR 0.012 0.001 TYR A 14 PHE 0.014 0.002 PHE A 498 TRP 0.004 0.001 TRP A 286 HIS 0.003 0.001 HIS A 558 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 6683) covalent geometry : angle 0.55547 ( 9263) hydrogen bonds : bond 0.12757 ( 314) hydrogen bonds : angle 4.50461 ( 868) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.9428 (OUTLIER) cc_final: 0.8429 (mp10) REVERT: A 117 MET cc_start: 0.9033 (ptt) cc_final: 0.8785 (ptt) REVERT: A 342 PHE cc_start: 0.6990 (p90) cc_final: 0.6195 (p90) REVERT: A 600 SER cc_start: 0.9047 (t) cc_final: 0.8460 (p) outliers start: 8 outliers final: 3 residues processed: 54 average time/residue: 0.0945 time to fit residues: 6.9050 Evaluate side-chains 43 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 599 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.0670 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.0020 chunk 27 optimal weight: 0.8980 overall best weight: 0.5126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 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 = 0.4254 r_free = 0.4254 target = 0.136854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.090241 restraints weight = 14116.418| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.70 r_work: 0.3219 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6683 Z= 0.099 Angle : 0.528 10.766 9263 Z= 0.256 Chirality : 0.035 0.140 1084 Planarity : 0.004 0.045 992 Dihedral : 14.982 73.696 1536 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.38 % Favored : 96.46 % Rotamer: Outliers : 1.82 % Allowed : 19.83 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.33), residues: 650 helix: 3.07 (0.28), residues: 321 sheet: 1.76 (0.54), residues: 89 loop : -1.17 (0.34), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 314 TYR 0.007 0.001 TYR A 472 PHE 0.007 0.001 PHE A 498 TRP 0.007 0.001 TRP A 286 HIS 0.003 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 6683) covalent geometry : angle 0.52751 ( 9263) hydrogen bonds : bond 0.03705 ( 314) hydrogen bonds : angle 3.49201 ( 868) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8911 (ptt) cc_final: 0.8710 (ptt) REVERT: A 315 GLU cc_start: 0.9241 (mm-30) cc_final: 0.8873 (mm-30) REVERT: A 342 PHE cc_start: 0.6932 (p90) cc_final: 0.6284 (p90) REVERT: A 397 ASP cc_start: 0.8717 (m-30) cc_final: 0.8502 (m-30) REVERT: A 590 PHE cc_start: 0.8954 (m-80) cc_final: 0.8200 (m-80) outliers start: 11 outliers final: 3 residues processed: 48 average time/residue: 0.0747 time to fit residues: 5.1979 Evaluate side-chains 42 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 526 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 48 optimal weight: 0.0070 chunk 59 optimal weight: 2.9990 overall best weight: 1.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.131528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.083657 restraints weight = 14080.190| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.70 r_work: 0.3044 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6683 Z= 0.172 Angle : 0.584 8.930 9263 Z= 0.293 Chirality : 0.037 0.140 1084 Planarity : 0.004 0.050 992 Dihedral : 14.790 73.727 1527 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.69 % Favored : 96.15 % Rotamer: Outliers : 1.98 % Allowed : 20.83 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.33), residues: 650 helix: 3.09 (0.28), residues: 314 sheet: 1.23 (0.52), residues: 95 loop : -1.37 (0.35), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 295 TYR 0.014 0.001 TYR A 14 PHE 0.018 0.002 PHE A 498 TRP 0.008 0.001 TRP A 286 HIS 0.004 0.001 HIS A 558 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 6683) covalent geometry : angle 0.58442 ( 9263) hydrogen bonds : bond 0.05653 ( 314) hydrogen bonds : angle 3.73255 ( 868) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8968 (ptt) cc_final: 0.8712 (ptt) REVERT: A 199 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8632 (mp) REVERT: A 282 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: A 315 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8871 (mm-30) REVERT: A 342 PHE cc_start: 0.7152 (p90) cc_final: 0.6624 (p90) REVERT: A 397 ASP cc_start: 0.8825 (m-30) cc_final: 0.8527 (m-30) REVERT: A 495 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7763 (ptmt) REVERT: A 530 PHE cc_start: 0.6617 (OUTLIER) cc_final: 0.4824 (p90) REVERT: A 590 PHE cc_start: 0.9013 (m-80) cc_final: 0.8428 (m-80) outliers start: 12 outliers final: 2 residues processed: 53 average time/residue: 0.0890 time to fit residues: 6.4026 Evaluate side-chains 45 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 530 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 63 optimal weight: 0.0670 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 32 optimal weight: 0.0010 chunk 25 optimal weight: 9.9990 chunk 44 optimal weight: 0.0770 chunk 41 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 overall best weight: 0.3884 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.133924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.086725 restraints weight = 14222.750| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.66 r_work: 0.3163 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6683 Z= 0.090 Angle : 0.525 10.968 9263 Z= 0.254 Chirality : 0.034 0.134 1084 Planarity : 0.004 0.047 992 Dihedral : 14.704 73.741 1527 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.77 % Favored : 97.08 % Rotamer: Outliers : 1.49 % Allowed : 21.49 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.33), residues: 650 helix: 3.09 (0.29), residues: 321 sheet: 1.19 (0.53), residues: 98 loop : -1.17 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 314 TYR 0.007 0.001 TYR A 160 PHE 0.021 0.001 PHE A 358 TRP 0.007 0.001 TRP A 286 HIS 0.001 0.000 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 6683) covalent geometry : angle 0.52507 ( 9263) hydrogen bonds : bond 0.03263 ( 314) hydrogen bonds : angle 3.26207 ( 868) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8857 (ptt) cc_final: 0.8650 (ptt) REVERT: A 299 LEU cc_start: 0.8558 (mm) cc_final: 0.8127 (tp) REVERT: A 315 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8796 (mm-30) REVERT: A 342 PHE cc_start: 0.6875 (p90) cc_final: 0.6453 (p90) REVERT: A 495 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7790 (ptmt) REVERT: A 530 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.4706 (p90) REVERT: A 590 PHE cc_start: 0.9005 (m-80) cc_final: 0.8585 (m-80) outliers start: 9 outliers final: 3 residues processed: 48 average time/residue: 0.0845 time to fit residues: 5.6613 Evaluate side-chains 43 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 530 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.129549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.081309 restraints weight = 14489.101| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.73 r_work: 0.3053 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6683 Z= 0.193 Angle : 0.612 11.551 9263 Z= 0.302 Chirality : 0.038 0.139 1084 Planarity : 0.004 0.051 992 Dihedral : 14.756 73.762 1527 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.46 % Favored : 95.38 % Rotamer: Outliers : 1.65 % Allowed : 21.49 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.33), residues: 650 helix: 3.20 (0.28), residues: 314 sheet: 1.26 (0.52), residues: 93 loop : -1.45 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 314 TYR 0.016 0.001 TYR A 14 PHE 0.018 0.002 PHE A 498 TRP 0.006 0.001 TRP A 286 HIS 0.004 0.001 HIS A 558 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 6683) covalent geometry : angle 0.61167 ( 9263) hydrogen bonds : bond 0.05714 ( 314) hydrogen bonds : angle 3.67477 ( 868) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.9006 (ptt) cc_final: 0.8756 (ptt) REVERT: A 199 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8700 (mp) REVERT: A 282 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: A 299 LEU cc_start: 0.8448 (mm) cc_final: 0.7998 (tp) REVERT: A 315 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8740 (mm-30) REVERT: A 342 PHE cc_start: 0.7028 (p90) cc_final: 0.6651 (p90) REVERT: A 495 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7787 (ptmt) REVERT: A 530 PHE cc_start: 0.6714 (OUTLIER) cc_final: 0.5057 (p90) outliers start: 10 outliers final: 3 residues processed: 48 average time/residue: 0.1028 time to fit residues: 6.5936 Evaluate side-chains 43 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 615 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 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 = 0.4111 r_free = 0.4111 target = 0.131604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.079425 restraints weight = 14591.677| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 4.14 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6683 Z= 0.119 Angle : 0.581 11.314 9263 Z= 0.282 Chirality : 0.036 0.138 1084 Planarity : 0.004 0.048 992 Dihedral : 14.719 73.760 1527 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.69 % Favored : 96.15 % Rotamer: Outliers : 1.16 % Allowed : 22.15 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.33), residues: 650 helix: 3.16 (0.28), residues: 320 sheet: 0.96 (0.50), residues: 100 loop : -1.47 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 314 TYR 0.010 0.001 TYR A 14 PHE 0.010 0.001 PHE A 498 TRP 0.007 0.001 TRP A 286 HIS 0.011 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6683) covalent geometry : angle 0.58115 ( 9263) hydrogen bonds : bond 0.04375 ( 314) hydrogen bonds : angle 3.41946 ( 868) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 LEU cc_start: 0.8416 (mm) cc_final: 0.8003 (tp) REVERT: A 315 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8750 (mm-30) REVERT: A 342 PHE cc_start: 0.6981 (p90) cc_final: 0.6693 (p90) REVERT: A 449 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8695 (tm-30) REVERT: A 495 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7600 (ptmt) REVERT: A 530 PHE cc_start: 0.6383 (OUTLIER) cc_final: 0.5062 (p90) outliers start: 7 outliers final: 1 residues processed: 43 average time/residue: 0.0769 time to fit residues: 4.8077 Evaluate side-chains 40 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 530 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 23 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 54 optimal weight: 0.0470 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.130866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.078196 restraints weight = 14469.578| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 4.14 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6683 Z= 0.159 Angle : 0.624 11.852 9263 Z= 0.301 Chirality : 0.037 0.141 1084 Planarity : 0.004 0.049 992 Dihedral : 14.728 73.817 1527 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.62 % Favored : 95.23 % Rotamer: Outliers : 1.65 % Allowed : 21.16 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.33), residues: 650 helix: 3.29 (0.28), residues: 314 sheet: 1.13 (0.52), residues: 93 loop : -1.48 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 232 TYR 0.014 0.001 TYR A 14 PHE 0.016 0.002 PHE A 358 TRP 0.006 0.001 TRP A 286 HIS 0.016 0.002 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 6683) covalent geometry : angle 0.62389 ( 9263) hydrogen bonds : bond 0.05377 ( 314) hydrogen bonds : angle 3.58612 ( 868) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.8335 (mt0) REVERT: A 299 LEU cc_start: 0.8431 (mm) cc_final: 0.8040 (tp) REVERT: A 397 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8514 (p0) REVERT: A 495 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7653 (ptmt) REVERT: A 530 PHE cc_start: 0.6470 (OUTLIER) cc_final: 0.5173 (p90) REVERT: A 600 SER cc_start: 0.9038 (OUTLIER) cc_final: 0.8746 (t) outliers start: 10 outliers final: 4 residues processed: 43 average time/residue: 0.0784 time to fit residues: 4.8158 Evaluate side-chains 44 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 615 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 2 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 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 = 0.4123 r_free = 0.4123 target = 0.132524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.080523 restraints weight = 14478.094| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 4.19 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6683 Z= 0.109 Angle : 0.597 12.768 9263 Z= 0.282 Chirality : 0.035 0.137 1084 Planarity : 0.004 0.049 992 Dihedral : 14.682 73.794 1527 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.38 % Favored : 96.46 % Rotamer: Outliers : 1.65 % Allowed : 22.15 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.33), residues: 650 helix: 3.17 (0.29), residues: 321 sheet: 0.93 (0.51), residues: 98 loop : -1.40 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 232 TYR 0.009 0.001 TYR A 14 PHE 0.013 0.001 PHE A 358 TRP 0.004 0.001 TRP A 286 HIS 0.015 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 6683) covalent geometry : angle 0.59659 ( 9263) hydrogen bonds : bond 0.04000 ( 314) hydrogen bonds : angle 3.35052 ( 868) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6462 (pm20) REVERT: A 299 LEU cc_start: 0.8427 (mm) cc_final: 0.8054 (tp) REVERT: A 449 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8681 (tm-30) REVERT: A 495 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7609 (ptmt) REVERT: A 530 PHE cc_start: 0.6238 (OUTLIER) cc_final: 0.4974 (p90) REVERT: A 600 SER cc_start: 0.9032 (OUTLIER) cc_final: 0.8724 (t) REVERT: A 632 MET cc_start: 0.8054 (tmm) cc_final: 0.7693 (ttp) outliers start: 10 outliers final: 2 residues processed: 46 average time/residue: 0.0843 time to fit residues: 5.3847 Evaluate side-chains 43 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 600 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 23 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 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 323 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 = 0.4104 r_free = 0.4104 target = 0.131780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.079548 restraints weight = 14686.268| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 4.19 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6683 Z= 0.125 Angle : 0.620 17.070 9263 Z= 0.293 Chirality : 0.036 0.139 1084 Planarity : 0.004 0.049 992 Dihedral : 14.669 73.822 1527 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.31 % Favored : 95.54 % Rotamer: Outliers : 1.49 % Allowed : 22.48 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.33), residues: 650 helix: 3.16 (0.29), residues: 321 sheet: 0.99 (0.50), residues: 99 loop : -1.45 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 232 TYR 0.011 0.001 TYR A 14 PHE 0.029 0.002 PHE A 358 TRP 0.002 0.001 TRP A 105 HIS 0.014 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6683) covalent geometry : angle 0.61964 ( 9263) hydrogen bonds : bond 0.04491 ( 314) hydrogen bonds : angle 3.44877 ( 868) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8697 (mt0) REVERT: A 299 LEU cc_start: 0.8365 (mm) cc_final: 0.7991 (tp) REVERT: A 397 ASP cc_start: 0.8788 (m-30) cc_final: 0.8547 (p0) REVERT: A 449 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8676 (tm-30) REVERT: A 495 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7637 (ptmt) REVERT: A 530 PHE cc_start: 0.6207 (OUTLIER) cc_final: 0.4925 (p90) REVERT: A 600 SER cc_start: 0.9050 (OUTLIER) cc_final: 0.8750 (t) REVERT: A 632 MET cc_start: 0.8114 (tmm) cc_final: 0.7761 (ttp) outliers start: 9 outliers final: 2 residues processed: 48 average time/residue: 0.0788 time to fit residues: 5.3991 Evaluate side-chains 46 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 600 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 65 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 29 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 44 optimal weight: 0.0030 chunk 4 optimal weight: 0.6980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 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 = 0.4133 r_free = 0.4133 target = 0.133200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.080983 restraints weight = 14443.634| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 4.23 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6683 Z= 0.101 Angle : 0.617 16.525 9263 Z= 0.288 Chirality : 0.035 0.137 1084 Planarity : 0.004 0.048 992 Dihedral : 14.636 73.809 1527 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.38 % Favored : 96.46 % Rotamer: Outliers : 0.99 % Allowed : 22.81 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.33), residues: 650 helix: 3.21 (0.29), residues: 321 sheet: 1.11 (0.51), residues: 99 loop : -1.34 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 232 TYR 0.008 0.001 TYR A 14 PHE 0.032 0.001 PHE A 358 TRP 0.003 0.001 TRP A 286 HIS 0.013 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 6683) covalent geometry : angle 0.61656 ( 9263) hydrogen bonds : bond 0.03718 ( 314) hydrogen bonds : angle 3.30734 ( 868) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8620 (mt0) REVERT: A 299 LEU cc_start: 0.8379 (mm) cc_final: 0.8014 (tp) REVERT: A 397 ASP cc_start: 0.8789 (m-30) cc_final: 0.8548 (p0) REVERT: A 449 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8653 (tm-30) REVERT: A 495 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7554 (ptmt) REVERT: A 530 PHE cc_start: 0.6161 (OUTLIER) cc_final: 0.4958 (p90) REVERT: A 600 SER cc_start: 0.9001 (OUTLIER) cc_final: 0.8686 (t) REVERT: A 632 MET cc_start: 0.8045 (tmm) cc_final: 0.7691 (ttp) outliers start: 6 outliers final: 1 residues processed: 43 average time/residue: 0.0770 time to fit residues: 4.8018 Evaluate side-chains 43 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 600 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 18 optimal weight: 0.0050 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 66 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 41 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN ** A 323 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 = 0.4143 r_free = 0.4143 target = 0.133357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.082943 restraints weight = 14424.505| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 4.07 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6683 Z= 0.104 Angle : 0.616 15.944 9263 Z= 0.294 Chirality : 0.035 0.142 1084 Planarity : 0.004 0.048 992 Dihedral : 14.607 73.818 1527 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.23 % Favored : 96.62 % Rotamer: Outliers : 1.32 % Allowed : 22.31 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.34), residues: 650 helix: 3.21 (0.29), residues: 323 sheet: 1.23 (0.51), residues: 99 loop : -1.24 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 232 TYR 0.009 0.001 TYR A 160 PHE 0.010 0.001 PHE A 400 TRP 0.002 0.000 TRP A 105 HIS 0.012 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 6683) covalent geometry : angle 0.61622 ( 9263) hydrogen bonds : bond 0.03668 ( 314) hydrogen bonds : angle 3.32590 ( 868) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1978.25 seconds wall clock time: 34 minutes 38.44 seconds (2078.44 seconds total)