Starting phenix.real_space_refine on Thu Mar 13 00:00:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c8k_30306/03_2025/7c8k_30306.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c8k_30306/03_2025/7c8k_30306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7c8k_30306/03_2025/7c8k_30306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c8k_30306/03_2025/7c8k_30306.map" model { file = "/net/cci-nas-00/data/ceres_data/7c8k_30306/03_2025/7c8k_30306.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c8k_30306/03_2025/7c8k_30306.cif" } resolution = 3.2 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4459 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 29 5.16 5 C 3104 2.51 5 N 804 2.21 5 O 915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4853 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4782 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 566} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.48, per 1000 atoms: 0.72 Number of scatterers: 4853 At special positions: 0 Unit cell: (78.5062, 87.45, 79.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 29 16.00 O 915 8.00 N 804 7.00 C 3104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 701 " - " ASN A 53 " " NAG A 702 " - " ASN A 90 " " NAG A 706 " - " ASN A 329 " " NAG B 1 " - " ASN A 546 " Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 517.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 705 " pdb="ZN ZN A 705 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 705 " - pdb=" NE2 HIS A 374 " 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1124 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 3 sheets defined 66.6% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.564A pdb=" N GLU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 82 removed outlier: 3.688A pdb=" N GLN A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.690A pdb=" N LYS A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.573A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 249 removed outlier: 3.639A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N MET A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 224 " --> pdb=" O ASP A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.557A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.698A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.772A pdb=" N ASN A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 4.119A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 removed outlier: 3.521A pdb=" N LEU A 503 " --> pdb=" O PRO A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.953A pdb=" N ASN A 508 " --> pdb=" O HIS A 505 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP A 509 " --> pdb=" O VAL A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 509' Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.717A pdb=" N ARG A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.705A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.652A pdb=" N ILE A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.562A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 258 hydrogen bonds defined for protein. 753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1541 1.34 - 1.46: 1058 1.46 - 1.58: 2340 1.58 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 4989 Sorted by residual: bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" C1 NAG A 706 " pdb=" O5 NAG A 706 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.86e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.39e+00 ... (remaining 4984 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 6659 1.72 - 3.44: 99 3.44 - 5.16: 12 5.16 - 6.88: 2 6.88 - 8.60: 1 Bond angle restraints: 6773 Sorted by residual: angle pdb=" N VAL A 107 " pdb=" CA VAL A 107 " pdb=" C VAL A 107 " ideal model delta sigma weight residual 113.71 109.31 4.40 9.50e-01 1.11e+00 2.15e+01 angle pdb=" N ILE A 544 " pdb=" CA ILE A 544 " pdb=" C ILE A 544 " ideal model delta sigma weight residual 113.22 109.12 4.10 1.23e+00 6.61e-01 1.11e+01 angle pdb=" C CYS A 344 " pdb=" N HIS A 345 " pdb=" CA HIS A 345 " ideal model delta sigma weight residual 122.21 130.81 -8.60 2.87e+00 1.21e-01 8.99e+00 angle pdb=" C ILE A 233 " pdb=" N LYS A 234 " pdb=" CA LYS A 234 " ideal model delta sigma weight residual 121.62 125.48 -3.86 1.57e+00 4.06e-01 6.04e+00 angle pdb=" CA VAL A 107 " pdb=" C VAL A 107 " pdb=" N LEU A 108 " ideal model delta sigma weight residual 119.87 116.80 3.07 1.34e+00 5.57e-01 5.24e+00 ... (remaining 6768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 2752 17.16 - 34.33: 211 34.33 - 51.49: 42 51.49 - 68.65: 6 68.65 - 85.81: 10 Dihedral angle restraints: 3021 sinusoidal: 1273 harmonic: 1748 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -124.47 38.47 1 1.00e+01 1.00e-02 2.08e+01 dihedral pdb=" CB GLU A 310 " pdb=" CG GLU A 310 " pdb=" CD GLU A 310 " pdb=" OE1 GLU A 310 " ideal model delta sinusoidal sigma weight residual 0.00 -85.81 85.81 1 3.00e+01 1.11e-03 9.89e+00 dihedral pdb=" CB GLU A 208 " pdb=" CG GLU A 208 " pdb=" CD GLU A 208 " pdb=" OE1 GLU A 208 " ideal model delta sinusoidal sigma weight residual 0.00 -83.89 83.89 1 3.00e+01 1.11e-03 9.53e+00 ... (remaining 3018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 719 0.134 - 0.267: 2 0.267 - 0.401: 0 0.401 - 0.535: 0 0.535 - 0.668: 1 Chirality restraints: 722 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-02 2.50e+03 1.12e+03 chirality pdb=" CB VAL A 581 " pdb=" CA VAL A 581 " pdb=" CG1 VAL A 581 " pdb=" CG2 VAL A 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA VAL A 318 " pdb=" N VAL A 318 " pdb=" C VAL A 318 " pdb=" CB VAL A 318 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 719 not shown) Planarity restraints: 865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 582 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 583 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " 0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO A 146 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " 0.016 5.00e-02 4.00e+02 2.44e-02 9.55e-01 pdb=" N PRO A 235 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " 0.014 5.00e-02 4.00e+02 ... (remaining 862 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 38 2.58 - 3.16: 3919 3.16 - 3.74: 7832 3.74 - 4.32: 10681 4.32 - 4.90: 17675 Nonbonded interactions: 40145 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 705 " model vdw 2.001 2.230 nonbonded pdb=" OD1 ASP A 227 " pdb=" OH TYR A 454 " model vdw 2.295 3.040 nonbonded pdb=" OD1 ASP A 543 " pdb=" OG SER A 545 " model vdw 2.298 3.040 nonbonded pdb=" O TRP A 48 " pdb=" OG1 THR A 52 " model vdw 2.301 3.040 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.303 3.040 ... (remaining 40140 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.770 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 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 : 0.002 0.029 4989 Z= 0.149 Angle : 0.515 8.603 6773 Z= 0.293 Chirality : 0.045 0.668 722 Planarity : 0.003 0.041 861 Dihedral : 13.488 85.814 1888 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.52 (0.31), residues: 594 helix: -0.16 (0.26), residues: 353 sheet: None (None), residues: 0 loop : -2.29 (0.33), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 473 HIS 0.001 0.000 HIS A 374 PHE 0.004 0.001 PHE A 400 TYR 0.005 0.001 TYR A 237 ARG 0.001 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8357 (m-40) cc_final: 0.8134 (m-40) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1888 time to fit residues: 22.5938 Evaluate side-chains 51 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.102604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.085290 restraints weight = 10252.113| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.39 r_work: 0.3147 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4989 Z= 0.175 Angle : 0.514 6.455 6773 Z= 0.255 Chirality : 0.041 0.157 722 Planarity : 0.004 0.055 861 Dihedral : 3.881 30.607 751 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.60 % Allowed : 7.60 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.16 (0.34), residues: 594 helix: 1.17 (0.28), residues: 355 sheet: -2.50 (1.15), residues: 12 loop : -1.47 (0.36), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 473 HIS 0.003 0.001 HIS A 526 PHE 0.013 0.002 PHE A 400 TYR 0.012 0.001 TYR A 381 ARG 0.005 0.001 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8803 (m-40) cc_final: 0.8555 (m-40) REVERT: A 609 ASP cc_start: 0.8322 (p0) cc_final: 0.8120 (p0) outliers start: 3 outliers final: 1 residues processed: 59 average time/residue: 0.1238 time to fit residues: 10.5216 Evaluate side-chains 48 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 58 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.102762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.086070 restraints weight = 9970.077| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.27 r_work: 0.3161 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4989 Z= 0.139 Angle : 0.479 6.467 6773 Z= 0.235 Chirality : 0.039 0.127 722 Planarity : 0.004 0.053 861 Dihedral : 3.289 18.478 751 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.80 % Allowed : 9.40 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.73 (0.34), residues: 594 helix: 1.64 (0.28), residues: 360 sheet: -2.47 (1.17), residues: 12 loop : -1.32 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 473 HIS 0.003 0.001 HIS A 526 PHE 0.007 0.001 PHE A 523 TYR 0.021 0.001 TYR A 50 ARG 0.003 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8860 (m-40) cc_final: 0.8617 (m-40) REVERT: A 194 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.6171 (t80) REVERT: A 609 ASP cc_start: 0.8351 (p0) cc_final: 0.8124 (p0) outliers start: 4 outliers final: 2 residues processed: 56 average time/residue: 0.1217 time to fit residues: 10.0676 Evaluate side-chains 49 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 364 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 42 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.0000 chunk 23 optimal weight: 8.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.102732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.085872 restraints weight = 10033.211| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.30 r_work: 0.3159 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 4989 Z= 0.140 Angle : 0.472 6.264 6773 Z= 0.233 Chirality : 0.038 0.129 722 Planarity : 0.004 0.053 861 Dihedral : 3.129 14.222 751 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.00 % Allowed : 10.20 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.00 (0.35), residues: 594 helix: 1.78 (0.28), residues: 366 sheet: -2.54 (1.11), residues: 12 loop : -1.12 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.002 0.000 HIS A 526 PHE 0.008 0.001 PHE A 523 TYR 0.028 0.001 TYR A 50 ARG 0.002 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8880 (m-40) cc_final: 0.8627 (m-40) REVERT: A 609 ASP cc_start: 0.8354 (p0) cc_final: 0.8140 (p0) outliers start: 5 outliers final: 4 residues processed: 55 average time/residue: 0.1169 time to fit residues: 9.6415 Evaluate side-chains 52 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 509 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.097658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.080610 restraints weight = 10104.272| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.27 r_work: 0.3061 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4989 Z= 0.238 Angle : 0.538 6.383 6773 Z= 0.272 Chirality : 0.042 0.178 722 Planarity : 0.004 0.055 861 Dihedral : 3.542 17.506 751 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.40 % Allowed : 11.20 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.13 (0.35), residues: 594 helix: 1.77 (0.28), residues: 368 sheet: -1.88 (1.20), residues: 10 loop : -0.90 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 478 HIS 0.007 0.001 HIS A 526 PHE 0.020 0.002 PHE A 400 TYR 0.034 0.002 TYR A 50 ARG 0.002 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 GLN cc_start: 0.7809 (pm20) cc_final: 0.7452 (pp30) outliers start: 7 outliers final: 3 residues processed: 54 average time/residue: 0.1231 time to fit residues: 9.7564 Evaluate side-chains 47 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 364 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 18 optimal weight: 0.8980 chunk 55 optimal weight: 0.0470 chunk 44 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.098605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.081440 restraints weight = 10103.870| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.31 r_work: 0.3064 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4989 Z= 0.174 Angle : 0.504 6.579 6773 Z= 0.252 Chirality : 0.040 0.169 722 Planarity : 0.004 0.052 861 Dihedral : 3.440 17.958 751 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.20 % Allowed : 12.00 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.23 (0.35), residues: 594 helix: 1.84 (0.28), residues: 368 sheet: -2.27 (1.14), residues: 10 loop : -0.84 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 478 HIS 0.003 0.001 HIS A 526 PHE 0.011 0.001 PHE A 400 TYR 0.024 0.001 TYR A 50 ARG 0.002 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 TRP cc_start: 0.8324 (m100) cc_final: 0.7275 (m100) outliers start: 6 outliers final: 5 residues processed: 52 average time/residue: 0.1187 time to fit residues: 9.2580 Evaluate side-chains 51 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 420 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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: 53.9693 > 50: distance: 1 - 24: 5.999 distance: 5 - 29: 6.436 distance: 9 - 37: 6.939 distance: 17 - 24: 4.038 distance: 18 - 43: 6.482 distance: 24 - 25: 9.753 distance: 25 - 26: 15.326 distance: 25 - 28: 5.436 distance: 26 - 27: 12.619 distance: 26 - 29: 10.596 distance: 27 - 54: 6.403 distance: 29 - 30: 6.635 distance: 30 - 31: 16.066 distance: 30 - 33: 5.676 distance: 31 - 32: 8.399 distance: 31 - 37: 7.959 distance: 32 - 62: 13.513 distance: 34 - 35: 6.143 distance: 34 - 36: 7.308 distance: 37 - 38: 7.669 distance: 38 - 39: 3.653 distance: 38 - 41: 9.412 distance: 39 - 40: 5.568 distance: 41 - 42: 11.149 distance: 42 - 112: 5.111 distance: 43 - 44: 5.598 distance: 44 - 45: 11.299 distance: 44 - 47: 9.627 distance: 45 - 46: 10.409 distance: 45 - 54: 4.116 distance: 48 - 49: 5.615 distance: 49 - 50: 3.982 distance: 51 - 52: 3.136 distance: 51 - 53: 3.325 distance: 54 - 55: 4.821 distance: 55 - 56: 9.139 distance: 55 - 58: 14.804 distance: 56 - 57: 14.183 distance: 56 - 62: 31.591 distance: 58 - 59: 14.038 distance: 58 - 60: 19.032 distance: 59 - 61: 13.576 distance: 62 - 63: 31.812 distance: 63 - 64: 13.213 distance: 63 - 66: 22.065 distance: 64 - 65: 42.359 distance: 64 - 67: 9.355 distance: 67 - 68: 23.296 distance: 68 - 69: 9.268 distance: 68 - 71: 13.203 distance: 69 - 70: 6.581 distance: 69 - 72: 18.668 distance: 72 - 73: 17.026 distance: 73 - 74: 11.903 distance: 73 - 76: 6.033 distance: 74 - 75: 16.985 distance: 74 - 82: 16.011 distance: 76 - 77: 18.857 distance: 77 - 78: 24.355 distance: 77 - 79: 22.567 distance: 78 - 80: 21.049 distance: 79 - 81: 16.766 distance: 80 - 81: 19.564 distance: 82 - 83: 13.004 distance: 83 - 84: 29.933 distance: 83 - 86: 34.159 distance: 84 - 85: 13.819 distance: 84 - 87: 15.742 distance: 87 - 88: 40.006 distance: 88 - 89: 4.638 distance: 89 - 90: 28.170 distance: 89 - 91: 13.977