Starting phenix.real_space_refine on Sat May 10 14:56:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mx5_48710/05_2025/9mx5_48710.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mx5_48710/05_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_48710/05_2025/9mx5_48710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mx5_48710/05_2025/9mx5_48710.map" model { file = "/net/cci-nas-00/data/ceres_data/9mx5_48710/05_2025/9mx5_48710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mx5_48710/05_2025/9mx5_48710.cif" } resolution = 3.1 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= 0.012 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.65, per 1000 atoms: 0.72 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: 1.63 Conformation dependent library (CDL) restraints added in 696.8 milliseconds 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: 2.00 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: 2.27 Time building geometry restraints manager: 1.87 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.420 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.140 ------------------------------------------------------------------------------- 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 (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: 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 TRP 0.004 0.001 TRP A 286 HIS 0.003 0.001 HIS A 558 PHE 0.014 0.002 PHE A 498 TYR 0.012 0.001 TYR A 14 ARG 0.002 0.000 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.12757 ( 314) hydrogen bonds : angle 4.50461 ( 868) covalent geometry : bond 0.00329 ( 6683) covalent geometry : angle 0.55547 ( 9263) *********************** 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 : 0.611 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: 0.1986 time to fit residues: 14.5221 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 : 0.717 ------------------------------------------------------------------------------- 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 58 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.0980 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.0070 chunk 40 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 = 0.4251 r_free = 0.4251 target = 0.136728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.090008 restraints weight = 13973.951| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.71 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6683 Z= 0.099 Angle : 0.523 10.302 9263 Z= 0.255 Chirality : 0.035 0.140 1084 Planarity : 0.004 0.044 992 Dihedral : 14.978 73.659 1536 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.38 % Favored : 96.46 % Rotamer: Outliers : 1.82 % Allowed : 20.50 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.16 (0.33), residues: 650 helix: 3.08 (0.28), residues: 321 sheet: 1.81 (0.54), residues: 89 loop : -1.17 (0.34), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 286 HIS 0.002 0.001 HIS A 83 PHE 0.007 0.001 PHE A 498 TYR 0.007 0.001 TYR A 14 ARG 0.002 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 314) hydrogen bonds : angle 3.52369 ( 868) covalent geometry : bond 0.00206 ( 6683) covalent geometry : angle 0.52322 ( 9263) *********************** 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 : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8820 (ptt) cc_final: 0.8619 (ptt) REVERT: A 315 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8802 (mm-30) REVERT: A 342 PHE cc_start: 0.6845 (p90) cc_final: 0.6207 (p90) REVERT: A 397 ASP cc_start: 0.8574 (m-30) cc_final: 0.8325 (m-30) REVERT: A 590 PHE cc_start: 0.9001 (m-80) cc_final: 0.8234 (m-80) outliers start: 11 outliers final: 3 residues processed: 48 average time/residue: 0.1667 time to fit residues: 11.4145 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 : 0.660 ------------------------------------------------------------------------------- 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 0 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 0.0980 chunk 33 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.130377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.082329 restraints weight = 14207.320| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.70 r_work: 0.3014 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6683 Z= 0.218 Angle : 0.631 9.295 9263 Z= 0.318 Chirality : 0.039 0.142 1084 Planarity : 0.005 0.052 992 Dihedral : 14.846 73.740 1527 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.00 % Favored : 95.85 % Rotamer: Outliers : 2.31 % Allowed : 20.50 % 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 (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: 1.69 (0.32), residues: 650 helix: 2.92 (0.28), residues: 314 sheet: 1.08 (0.51), residues: 95 loop : -1.44 (0.35), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 286 HIS 0.005 0.001 HIS A 558 PHE 0.021 0.002 PHE A 498 TYR 0.016 0.002 TYR A 14 ARG 0.012 0.001 ARG A 295 Details of bonding type rmsd hydrogen bonds : bond 0.06422 ( 314) hydrogen bonds : angle 3.92289 ( 868) covalent geometry : bond 0.00512 ( 6683) covalent geometry : angle 0.63069 ( 9263) *********************** 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 52 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8983 (ptt) cc_final: 0.8721 (ptt) REVERT: A 282 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: A 315 GLU cc_start: 0.9269 (mm-30) cc_final: 0.8885 (mm-30) REVERT: A 342 PHE cc_start: 0.7173 (p90) cc_final: 0.6657 (p90) REVERT: A 397 ASP cc_start: 0.8826 (m-30) cc_final: 0.8533 (m-30) REVERT: A 495 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7741 (ptmt) REVERT: A 530 PHE cc_start: 0.6761 (OUTLIER) cc_final: 0.4927 (p90) REVERT: A 632 MET cc_start: 0.8636 (tmm) cc_final: 0.8298 (ttp) outliers start: 14 outliers final: 4 residues processed: 52 average time/residue: 0.2008 time to fit residues: 14.0100 Evaluate side-chains 42 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 92 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4173 r_free = 0.4173 target = 0.131348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.083539 restraints weight = 14271.107| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.68 r_work: 0.3096 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2228 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= 0.114 Angle : 0.551 10.724 9263 Z= 0.271 Chirality : 0.036 0.135 1084 Planarity : 0.004 0.049 992 Dihedral : 14.766 73.742 1527 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.38 % Favored : 96.46 % Rotamer: Outliers : 0.83 % Allowed : 21.49 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.88 (0.33), residues: 650 helix: 3.12 (0.28), residues: 314 sheet: 0.84 (0.50), residues: 102 loop : -1.34 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 286 HIS 0.002 0.001 HIS A 630 PHE 0.017 0.001 PHE A 358 TYR 0.010 0.001 TYR A 14 ARG 0.002 0.000 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 314) hydrogen bonds : angle 3.49314 ( 868) covalent geometry : bond 0.00253 ( 6683) covalent geometry : angle 0.55124 ( 9263) *********************** 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 46 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8933 (ptt) cc_final: 0.8715 (ptt) REVERT: A 282 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: A 299 LEU cc_start: 0.8608 (mm) cc_final: 0.8175 (tp) REVERT: A 315 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8807 (mm-30) REVERT: A 342 PHE cc_start: 0.7011 (p90) cc_final: 0.6600 (p90) REVERT: A 495 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7779 (ptmt) REVERT: A 530 PHE cc_start: 0.6708 (OUTLIER) cc_final: 0.4900 (p90) REVERT: A 590 PHE cc_start: 0.9073 (m-80) cc_final: 0.8593 (m-80) outliers start: 5 outliers final: 1 residues processed: 46 average time/residue: 0.2313 time to fit residues: 14.2398 Evaluate side-chains 44 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 615 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 18 optimal weight: 0.0070 chunk 0 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 32 optimal weight: 0.0070 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 0.9820 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.131138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.083570 restraints weight = 14346.633| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.67 r_work: 0.3083 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2424 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= 0.124 Angle : 0.562 10.937 9263 Z= 0.273 Chirality : 0.036 0.140 1084 Planarity : 0.004 0.048 992 Dihedral : 14.728 73.760 1527 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.15 % Favored : 95.69 % Rotamer: Outliers : 1.82 % Allowed : 21.49 % 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 (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: 1.99 (0.33), residues: 650 helix: 3.25 (0.28), residues: 314 sheet: 0.79 (0.50), residues: 102 loop : -1.30 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 286 HIS 0.002 0.001 HIS A 558 PHE 0.011 0.001 PHE A 498 TYR 0.011 0.001 TYR A 14 ARG 0.002 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.04491 ( 314) hydrogen bonds : angle 3.43493 ( 868) covalent geometry : bond 0.00284 ( 6683) covalent geometry : angle 0.56224 ( 9263) *********************** 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 50 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: A 299 LEU cc_start: 0.8523 (mm) cc_final: 0.8042 (tp) REVERT: A 315 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8768 (mm-30) REVERT: A 342 PHE cc_start: 0.6960 (p90) cc_final: 0.6601 (p90) REVERT: A 495 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7803 (ptmt) REVERT: A 530 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.5026 (p90) REVERT: A 589 MET cc_start: 0.7498 (mmm) cc_final: 0.7291 (mmm) REVERT: A 632 MET cc_start: 0.8447 (tmm) cc_final: 0.8073 (ttp) outliers start: 11 outliers final: 4 residues processed: 49 average time/residue: 0.2158 time to fit residues: 14.2327 Evaluate side-chains 42 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 92 VAL 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 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 33 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 3 optimal weight: 0.0270 chunk 18 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.132810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.085448 restraints weight = 14126.906| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.71 r_work: 0.3115 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6683 Z= 0.106 Angle : 0.566 11.912 9263 Z= 0.273 Chirality : 0.035 0.137 1084 Planarity : 0.004 0.047 992 Dihedral : 14.702 73.754 1527 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.85 % Favored : 96.00 % Rotamer: Outliers : 1.32 % Allowed : 21.49 % 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 (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: 1.98 (0.33), residues: 650 helix: 3.17 (0.28), residues: 320 sheet: 0.89 (0.50), residues: 102 loop : -1.35 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 286 HIS 0.012 0.001 HIS A 289 PHE 0.030 0.001 PHE A 358 TYR 0.009 0.001 TYR A 14 ARG 0.002 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 314) hydrogen bonds : angle 3.34674 ( 868) covalent geometry : bond 0.00234 ( 6683) covalent geometry : angle 0.56599 ( 9263) *********************** 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 48 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 LEU cc_start: 0.8461 (mm) cc_final: 0.8013 (tp) REVERT: A 315 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8777 (mm-30) REVERT: A 342 PHE cc_start: 0.6868 (p90) cc_final: 0.6568 (p90) REVERT: A 449 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8801 (tm-30) REVERT: A 495 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7811 (ptmt) REVERT: A 530 PHE cc_start: 0.6659 (OUTLIER) cc_final: 0.4989 (p90) outliers start: 8 outliers final: 3 residues processed: 47 average time/residue: 0.1953 time to fit residues: 12.6480 Evaluate side-chains 44 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 92 VAL 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.0542 > 50: distance: 21 - 149: 35.098 distance: 29 - 152: 36.144 distance: 32 - 164: 33.586 distance: 129 - 133: 33.681 distance: 135 - 136: 39.112 distance: 135 - 141: 40.828 distance: 137 - 138: 56.219 distance: 138 - 139: 39.342 distance: 142 - 143: 43.758 distance: 142 - 145: 39.872 distance: 143 - 144: 59.481 distance: 143 - 149: 43.844 distance: 145 - 146: 39.807 distance: 146 - 147: 41.187 distance: 149 - 150: 39.949 distance: 150 - 151: 68.934 distance: 150 - 153: 40.206 distance: 151 - 152: 40.615 distance: 151 - 157: 61.567 distance: 153 - 154: 57.015 distance: 154 - 155: 43.004 distance: 154 - 156: 39.655 distance: 157 - 158: 26.002 distance: 158 - 159: 41.072 distance: 158 - 161: 17.669 distance: 159 - 160: 36.618 distance: 159 - 164: 39.412 distance: 161 - 162: 18.409 distance: 161 - 163: 19.518 distance: 164 - 165: 53.811 distance: 165 - 166: 34.596 distance: 165 - 168: 54.909 distance: 166 - 167: 54.330 distance: 166 - 169: 56.655 distance: 170 - 171: 39.576 distance: 171 - 172: 39.773 distance: 171 - 176: 41.143 distance: 173 - 174: 40.203 distance: 177 - 178: 39.190 distance: 177 - 180: 41.090 distance: 178 - 182: 40.229 distance: 180 - 181: 38.950 distance: 183 - 184: 57.129 distance: 184 - 185: 39.959 distance: 184 - 189: 56.530 distance: 186 - 187: 50.656 distance: 190 - 191: 38.641 distance: 190 - 193: 39.035 distance: 191 - 192: 39.726 distance: 193 - 194: 39.328 distance: 193 - 195: 39.431 distance: 196 - 197: 39.921 distance: 197 - 198: 40.930 distance: 197 - 200: 56.191 distance: 198 - 205: 34.385 distance: 200 - 201: 40.569 distance: 201 - 202: 39.346 distance: 202 - 204: 39.553