Starting phenix.real_space_refine on Fri Jan 17 13:28:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xjw_38408/01_2025/8xjw_38408.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xjw_38408/01_2025/8xjw_38408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xjw_38408/01_2025/8xjw_38408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xjw_38408/01_2025/8xjw_38408.map" model { file = "/net/cci-nas-00/data/ceres_data/8xjw_38408/01_2025/8xjw_38408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xjw_38408/01_2025/8xjw_38408.cif" } resolution = 2.84 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= 0.070 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 5737 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 31 5.49 5 S 29 5.16 5 C 3882 2.51 5 N 1108 2.21 5 O 1197 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6248 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5595 Classifications: {'peptide': 690} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 23, 'TRANS': 666} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 338 Classifications: {'DNA': 16} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 15} Chain: "C" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 308 Classifications: {'RNA': 15} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 8} Link IDs: {'rna3p': 14} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1, 'water': 3} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 4.36, per 1000 atoms: 0.70 Number of scatterers: 6248 At special positions: 0 Unit cell: (73.186, 91.057, 107.226, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 29 16.00 P 31 15.00 O 1197 8.00 N 1108 7.00 C 3882 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: 2.01 Conformation dependent library (CDL) restraints added in 649.1 milliseconds 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1316 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 9 sheets defined 35.7% alpha, 21.3% beta 9 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 13 through 17 removed outlier: 3.789A pdb=" N LEU A 17 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'A' and resid 159 through 166 removed outlier: 3.557A pdb=" N MET A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 269 removed outlier: 3.693A pdb=" N LYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 288 removed outlier: 3.561A pdb=" N THR A 279 " --> pdb=" O ARG A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.519A pdb=" N ILE A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 408 through 413 removed outlier: 3.643A pdb=" N PHE A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 428 Processing helix chain 'A' and resid 432 through 442 Processing helix chain 'A' and resid 453 through 467 removed outlier: 3.761A pdb=" N ILE A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 464 " --> pdb=" O PHE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 488 Processing helix chain 'A' and resid 491 through 507 removed outlier: 3.763A pdb=" N THR A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 585 removed outlier: 3.696A pdb=" N LEU A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 611 removed outlier: 4.363A pdb=" N VAL A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 692 removed outlier: 3.730A pdb=" N ILE A 685 " --> pdb=" O PRO A 681 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 686 " --> pdb=" O PHE A 682 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 695 No H-bonds generated for 'chain 'A' and resid 693 through 695' Processing helix chain 'A' and resid 709 through 722 removed outlier: 3.935A pdb=" N LEU A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 removed outlier: 3.817A pdb=" N THR A 639 " --> pdb=" O ASN A 634 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 9 removed outlier: 3.738A pdb=" N GLN A 153 " --> pdb=" O TYR A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 7 through 9 removed outlier: 3.738A pdb=" N GLN A 153 " --> pdb=" O TYR A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 Processing sheet with id=AA6, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.666A pdb=" N THR A 646 " --> pdb=" O CYS A 657 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE A 591 " --> pdb=" O ASP A 618 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL A 620 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE A 593 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE A 622 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG A 595 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL A 528 " --> pdb=" O ASP A 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 535 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA9, first strand: chain 'A' and resid 379 through 382 removed outlier: 8.956A pdb=" N THR A 416 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS A 342 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU A 418 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER A 344 " --> pdb=" O LEU A 418 " (cutoff:3.500A) 246 hydrogen bonds defined for protein. 687 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1727 1.33 - 1.45: 1318 1.45 - 1.57: 3290 1.57 - 1.69: 60 1.69 - 1.81: 51 Bond restraints: 6446 Sorted by residual: bond pdb=" P DT B 1 " pdb=" OP3 DT B 1 " ideal model delta sigma weight residual 1.480 1.571 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" CG1 ILE A 95 " pdb=" CD1 ILE A 95 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.52e+00 bond pdb=" P DT B 1 " pdb=" OP2 DT B 1 " ideal model delta sigma weight residual 1.480 1.458 0.022 2.00e-02 2.50e+03 1.21e+00 bond pdb=" N PRO A 474 " pdb=" CA PRO A 474 " ideal model delta sigma weight residual 1.469 1.456 0.013 1.28e-02 6.10e+03 1.02e+00 bond pdb=" SD MET A 703 " pdb=" CE MET A 703 " ideal model delta sigma weight residual 1.791 1.769 0.022 2.50e-02 1.60e+03 7.98e-01 ... (remaining 6441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 8616 1.53 - 3.06: 196 3.06 - 4.59: 33 4.59 - 6.12: 6 6.12 - 7.65: 5 Bond angle restraints: 8856 Sorted by residual: angle pdb=" N PRO A 474 " pdb=" CA PRO A 474 " pdb=" CB PRO A 474 " ideal model delta sigma weight residual 103.25 110.90 -7.65 1.05e+00 9.07e-01 5.30e+01 angle pdb=" N ILE A 550 " pdb=" CA ILE A 550 " pdb=" C ILE A 550 " ideal model delta sigma weight residual 111.91 105.62 6.29 8.90e-01 1.26e+00 4.99e+01 angle pdb=" CG1 ILE A 619 " pdb=" CB ILE A 619 " pdb=" CG2 ILE A 619 " ideal model delta sigma weight residual 110.70 103.31 7.39 3.00e+00 1.11e-01 6.07e+00 angle pdb=" C ASN A 47 " pdb=" N ASP A 48 " pdb=" CA ASP A 48 " ideal model delta sigma weight residual 121.54 126.22 -4.68 1.91e+00 2.74e-01 6.00e+00 angle pdb=" C ILE A 457 " pdb=" N GLU A 458 " pdb=" CA GLU A 458 " ideal model delta sigma weight residual 120.72 116.87 3.85 1.67e+00 3.59e-01 5.32e+00 ... (remaining 8851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.64: 3584 27.64 - 55.27: 192 55.27 - 82.91: 30 82.91 - 110.54: 4 110.54 - 138.18: 1 Dihedral angle restraints: 3811 sinusoidal: 1776 harmonic: 2035 Sorted by residual: dihedral pdb=" CA ASN A 54 " pdb=" C ASN A 54 " pdb=" N GLN A 55 " pdb=" CA GLN A 55 " ideal model delta harmonic sigma weight residual 180.00 -160.67 -19.33 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" C4' DT B 13 " pdb=" C3' DT B 13 " pdb=" O3' DT B 13 " pdb=" P DT B 14 " ideal model delta sinusoidal sigma weight residual 220.00 81.82 138.18 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" CA GLN A 76 " pdb=" C GLN A 76 " pdb=" N LYS A 77 " pdb=" CA LYS A 77 " ideal model delta harmonic sigma weight residual 180.00 163.18 16.82 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 3808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 764 0.043 - 0.087: 172 0.087 - 0.130: 57 0.130 - 0.173: 7 0.173 - 0.217: 2 Chirality restraints: 1002 Sorted by residual: chirality pdb=" CB ILE A 619 " pdb=" CA ILE A 619 " pdb=" CG1 ILE A 619 " pdb=" CG2 ILE A 619 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA PRO A 474 " pdb=" N PRO A 474 " pdb=" C PRO A 474 " pdb=" CB PRO A 474 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CA GLN A 575 " pdb=" N GLN A 575 " pdb=" C GLN A 575 " pdb=" CB GLN A 575 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 999 not shown) Planarity restraints: 1013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT B 1 " 0.029 2.00e-02 2.50e+03 1.48e-02 5.49e+00 pdb=" N1 DT B 1 " -0.034 2.00e-02 2.50e+03 pdb=" C2 DT B 1 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT B 1 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DT B 1 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT B 1 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT B 1 " 0.013 2.00e-02 2.50e+03 pdb=" C5 DT B 1 " -0.004 2.00e-02 2.50e+03 pdb=" C7 DT B 1 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DT B 1 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 49 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO A 50 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 50 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 50 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 705 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO A 706 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 706 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 706 " -0.019 5.00e-02 4.00e+02 ... (remaining 1010 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 158 2.69 - 3.24: 5711 3.24 - 3.79: 9694 3.79 - 4.35: 13469 4.35 - 4.90: 21861 Nonbonded interactions: 50893 Sorted by model distance: nonbonded pdb=" CG1 VAL A 737 " pdb="MN MN A 801 " model vdw 2.132 2.740 nonbonded pdb=" OE1 GLN A 510 " pdb=" OG1 THR A 732 " model vdw 2.241 3.040 nonbonded pdb=" NZ LYS A 269 " pdb=" O2 DT B 6 " model vdw 2.248 3.120 nonbonded pdb=" OE1 GLN A 435 " pdb=" NE2 GLN A 723 " model vdw 2.259 3.120 nonbonded pdb=" OH TYR A 434 " pdb=" OP3 DT B 1 " model vdw 2.277 3.040 ... (remaining 50888 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.670 Find NCS groups from input model: 0.090 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:14.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 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 0.091 6446 Z= 0.185 Angle : 0.579 7.646 8856 Z= 0.325 Chirality : 0.042 0.217 1002 Planarity : 0.004 0.040 1013 Dihedral : 16.621 138.177 2495 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.56 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: -0.92 (0.32), residues: 684 helix: 0.12 (0.34), residues: 239 sheet: 0.48 (0.42), residues: 151 loop : -1.83 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 43 HIS 0.004 0.001 HIS A 590 PHE 0.010 0.001 PHE A 86 TYR 0.008 0.001 TYR A 363 ARG 0.002 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 163 MET cc_start: 0.4887 (mtt) cc_final: 0.4602 (mtm) REVERT: A 493 TYR cc_start: 0.6802 (t80) cc_final: 0.6548 (t80) REVERT: A 667 MET cc_start: 0.7941 (ttt) cc_final: 0.7643 (ttt) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 1.1822 time to fit residues: 124.7395 Evaluate side-chains 73 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN A 126 GLN A 257 GLN A 379 ASN A 638 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.208626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.165297 restraints weight = 6257.134| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.71 r_work: 0.3673 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6446 Z= 0.317 Angle : 0.703 7.809 8856 Z= 0.369 Chirality : 0.047 0.170 1002 Planarity : 0.004 0.042 1013 Dihedral : 16.756 134.961 1140 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 4.13 % Allowed : 10.74 % Favored : 85.12 % 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: -1.02 (0.31), residues: 684 helix: 0.17 (0.33), residues: 243 sheet: 0.27 (0.42), residues: 154 loop : -1.97 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 282 HIS 0.004 0.001 HIS A 356 PHE 0.017 0.002 PHE A 253 TYR 0.017 0.002 TYR A 307 ARG 0.005 0.000 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.623 Fit side-chains REVERT: A 38 HIS cc_start: 0.6482 (OUTLIER) cc_final: 0.5813 (p90) REVERT: A 163 MET cc_start: 0.5507 (mtt) cc_final: 0.4920 (mtm) REVERT: A 259 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6963 (tt0) REVERT: A 439 GLN cc_start: 0.6631 (mt0) cc_final: 0.6250 (mt0) outliers start: 25 outliers final: 6 residues processed: 92 average time/residue: 1.1504 time to fit residues: 111.5777 Evaluate side-chains 84 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 615 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 68.1631 > 50: distance: 23 - 194: 7.425 distance: 26 - 191: 9.158 distance: 39 - 177: 7.130 distance: 98 - 186: 6.157 distance: 101 - 183: 6.361 distance: 112 - 169: 5.921 distance: 115 - 166: 7.359 distance: 135 - 137: 4.569 distance: 137 - 138: 12.974 distance: 138 - 139: 8.846 distance: 138 - 141: 15.799 distance: 139 - 140: 30.309 distance: 139 - 145: 24.351 distance: 141 - 142: 18.736 distance: 142 - 143: 21.373 distance: 143 - 144: 26.032 distance: 145 - 146: 11.373 distance: 146 - 147: 25.462 distance: 146 - 149: 14.461 distance: 147 - 148: 31.694 distance: 147 - 150: 14.602 distance: 150 - 151: 5.974 distance: 151 - 152: 10.011 distance: 151 - 154: 12.491 distance: 152 - 153: 9.127 distance: 152 - 159: 7.511 distance: 154 - 155: 10.578 distance: 155 - 156: 5.700 distance: 156 - 157: 5.772 distance: 156 - 158: 6.876 distance: 159 - 160: 6.683 distance: 159 - 165: 6.052 distance: 160 - 161: 5.607 distance: 160 - 163: 13.005 distance: 161 - 162: 8.545 distance: 161 - 166: 3.410 distance: 163 - 164: 10.115 distance: 164 - 165: 11.401 distance: 166 - 167: 5.692 distance: 167 - 168: 4.263 distance: 168 - 169: 4.930 distance: 168 - 174: 3.189 distance: 170 - 171: 4.478 distance: 170 - 172: 4.998 distance: 171 - 173: 5.302 distance: 174 - 175: 4.630 distance: 175 - 176: 4.581 distance: 175 - 178: 5.922 distance: 176 - 177: 6.866 distance: 176 - 183: 7.814 distance: 178 - 179: 3.789 distance: 179 - 180: 5.599 distance: 181 - 182: 9.983 distance: 183 - 184: 4.282 distance: 184 - 185: 5.684 distance: 184 - 187: 3.863 distance: 185 - 186: 3.230 distance: 185 - 191: 8.528 distance: 187 - 188: 9.358 distance: 187 - 189: 3.586 distance: 188 - 190: 10.870 distance: 191 - 192: 7.322 distance: 192 - 193: 6.495 distance: 192 - 195: 4.716 distance: 193 - 194: 5.143 distance: 193 - 201: 4.406 distance: 195 - 196: 5.445 distance: 196 - 197: 8.100 distance: 196 - 198: 6.611 distance: 201 - 202: 6.274 distance: 202 - 203: 4.275 distance: 202 - 205: 3.913 distance: 203 - 204: 7.771 distance: 203 - 210: 7.325 distance: 205 - 206: 11.895 distance: 206 - 207: 9.662 distance: 207 - 208: 8.217 distance: 207 - 209: 9.154 distance: 210 - 211: 4.051 distance: 211 - 212: 9.109 distance: 211 - 214: 5.116 distance: 212 - 213: 6.318 distance: 212 - 217: 3.010 distance: 214 - 215: 12.665 distance: 214 - 216: 9.972