Starting phenix.real_space_refine on Wed Mar 12 12:23:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7roz_24610/03_2025/7roz_24610.cif Found real_map, /net/cci-nas-00/data/ceres_data/7roz_24610/03_2025/7roz_24610.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/7roz_24610/03_2025/7roz_24610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7roz_24610/03_2025/7roz_24610.map" model { file = "/net/cci-nas-00/data/ceres_data/7roz_24610/03_2025/7roz_24610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7roz_24610/03_2025/7roz_24610.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= 0.001 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: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 47 5.16 5 C 4897 2.51 5 N 1343 2.21 5 O 1486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 7774 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 7773 Classifications: {'peptide': 1064} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 38, 'TRANS': 1025} Chain breaks: 8 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 802 Unresolved non-hydrogen angles: 1015 Unresolved non-hydrogen dihedrals: 715 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 17, 'ASN:plan1': 3, 'TRP:plan': 5, 'ASP:plan': 8, 'PHE:plan': 15, 'GLU:plan': 20, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 487 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.53, per 1000 atoms: 0.71 Number of scatterers: 7774 At special positions: 0 Unit cell: (96.216, 102.124, 81.868, 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) S 47 16.00 Mg 1 11.99 O 1486 8.00 N 1343 7.00 C 4897 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: 2.16 Conformation dependent library (CDL) restraints added in 978.9 milliseconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2024 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 36.4% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 22 through 34 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 270 through 273 removed outlier: 3.538A pdb=" N ALA A 273 " --> pdb=" O LYS A 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 273' Processing helix chain 'A' and resid 295 through 305 Processing helix chain 'A' and resid 309 through 315 Processing helix chain 'A' and resid 315 through 325 Processing helix chain 'A' and resid 326 through 340 removed outlier: 3.858A pdb=" N GLN A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 357 Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 409 through 413 removed outlier: 5.768A pdb=" N SER A 413 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 434 removed outlier: 3.501A pdb=" N LEU A 433 " --> pdb=" O PRO A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 461 removed outlier: 3.541A pdb=" N ASN A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'A' and resid 494 through 503 removed outlier: 3.608A pdb=" N ILE A 498 " --> pdb=" O LYS A 494 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 521 removed outlier: 3.826A pdb=" N LEU A 521 " --> pdb=" O ARG A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 573 Processing helix chain 'A' and resid 632 through 643 Processing helix chain 'A' and resid 645 through 662 removed outlier: 3.840A pdb=" N PHE A 649 " --> pdb=" O GLU A 645 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN A 662 " --> pdb=" O SER A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 665 No H-bonds generated for 'chain 'A' and resid 663 through 665' Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.810A pdb=" N ALA A 669 " --> pdb=" O ASP A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 692 removed outlier: 3.519A pdb=" N GLN A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 720 Processing helix chain 'A' and resid 753 through 759 Processing helix chain 'A' and resid 802 through 807 removed outlier: 3.565A pdb=" N LYS A 806 " --> pdb=" O HIS A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 868 through 882 Processing helix chain 'A' and resid 884 through 897 Processing helix chain 'A' and resid 905 through 921 Processing helix chain 'A' and resid 958 through 969 removed outlier: 3.867A pdb=" N ARG A 962 " --> pdb=" O GLY A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 989 Processing helix chain 'A' and resid 998 through 1017 removed outlier: 4.113A pdb=" N HIS A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU A1008 " --> pdb=" O ASP A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1053 Processing helix chain 'A' and resid 1055 through 1067 Processing helix chain 'A' and resid 1077 through 1089 Processing helix chain 'A' and resid 1101 through 1106 removed outlier: 3.957A pdb=" N VAL A1106 " --> pdb=" O PHE A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1121 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 14 removed outlier: 3.983A pdb=" N ALA A 57 " --> pdb=" O ILE A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 169 removed outlier: 6.964A pdb=" N ARG A 105 " --> pdb=" O TRP A 135 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP A 135 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASP A 107 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG A 133 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE A 109 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU A 127 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 125 removed outlier: 6.176A pdb=" N PHE A 123 " --> pdb=" O VAL A 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 400 removed outlier: 5.339A pdb=" N LEU A 393 " --> pdb=" O TYR A 385 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR A 385 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY A 395 " --> pdb=" O ARG A 383 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 383 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N PHE A 415 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLN A 382 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 417 " --> pdb=" O GLN A 382 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N TRP A 485 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 467 " --> pdb=" O VAL A 464 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 526 through 530 removed outlier: 4.843A pdb=" N LEU A 618 " --> pdb=" O THR A 528 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN A 582 " --> pdb=" O THR A 621 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TRP A 623 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA A 580 " --> pdb=" O TRP A 623 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 593 " --> pdb=" O GLY A 558 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 627 through 628 removed outlier: 3.992A pdb=" N MET A 627 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG A 749 " --> pdb=" O CYS A 811 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N CYS A 811 " --> pdb=" O ARG A 749 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS A 734 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 627 through 628 removed outlier: 3.992A pdb=" N MET A 627 " --> pdb=" O ILE A 730 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 939 through 940 removed outlier: 6.219A pdb=" N PHE A 939 " --> pdb=" O TYR A 951 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 339 hydrogen bonds defined for protein. 963 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: 3.95 Time building geometry restraints manager: 2.54 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: 2631 1.34 - 1.46: 1298 1.46 - 1.57: 3893 1.57 - 1.69: 1 1.69 - 1.81: 72 Bond restraints: 7895 Sorted by residual: bond pdb=" CB PRO A 940 " pdb=" CG PRO A 940 " ideal model delta sigma weight residual 1.492 1.580 -0.088 5.00e-02 4.00e+02 3.11e+00 bond pdb=" CB GLN A 567 " pdb=" CG GLN A 567 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.79e-01 bond pdb=" C ASN A 784 " pdb=" N PRO A 785 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.75e-01 bond pdb=" CA GLU A 117 " pdb=" CB GLU A 117 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.54e-02 4.22e+03 6.76e-01 bond pdb=" CG LEU A 911 " pdb=" CD2 LEU A 911 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.96e-01 ... (remaining 7890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 10404 1.40 - 2.80: 257 2.80 - 4.20: 39 4.20 - 5.59: 10 5.59 - 6.99: 2 Bond angle restraints: 10712 Sorted by residual: angle pdb=" CA PRO A 940 " pdb=" N PRO A 940 " pdb=" CD PRO A 940 " ideal model delta sigma weight residual 112.00 106.81 5.19 1.40e+00 5.10e-01 1.37e+01 angle pdb=" N LYS A 610 " pdb=" CA LYS A 610 " pdb=" C LYS A 610 " ideal model delta sigma weight residual 114.04 110.14 3.90 1.24e+00 6.50e-01 9.88e+00 angle pdb=" C ASP A 119 " pdb=" N GLU A 120 " pdb=" CA GLU A 120 " ideal model delta sigma weight residual 121.54 127.05 -5.51 1.91e+00 2.74e-01 8.32e+00 angle pdb=" CA GLU A 117 " pdb=" CB GLU A 117 " pdb=" CG GLU A 117 " ideal model delta sigma weight residual 114.10 119.42 -5.32 2.00e+00 2.50e-01 7.07e+00 angle pdb=" C VAL A 956 " pdb=" N PHE A 957 " pdb=" CA PHE A 957 " ideal model delta sigma weight residual 122.61 126.38 -3.77 1.56e+00 4.11e-01 5.85e+00 ... (remaining 10707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.78: 4299 15.78 - 31.55: 361 31.55 - 47.33: 103 47.33 - 63.11: 17 63.11 - 78.88: 7 Dihedral angle restraints: 4787 sinusoidal: 1689 harmonic: 3098 Sorted by residual: dihedral pdb=" CA VAL A 66 " pdb=" C VAL A 66 " pdb=" N LYS A 67 " pdb=" CA LYS A 67 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA PRO A 851 " pdb=" C PRO A 851 " pdb=" N PRO A 852 " pdb=" CA PRO A 852 " ideal model delta harmonic sigma weight residual 180.00 -161.62 -18.38 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA SER A 68 " pdb=" C SER A 68 " pdb=" N ARG A 69 " pdb=" CA ARG A 69 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 4784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 843 0.035 - 0.069: 289 0.069 - 0.103: 98 0.103 - 0.138: 33 0.138 - 0.172: 3 Chirality restraints: 1266 Sorted by residual: chirality pdb=" CB ILE A 539 " pdb=" CA ILE A 539 " pdb=" CG1 ILE A 539 " pdb=" CG2 ILE A 539 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" CB ILE A 96 " pdb=" CA ILE A 96 " pdb=" CG1 ILE A 96 " pdb=" CG2 ILE A 96 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CA GLN A 567 " pdb=" N GLN A 567 " pdb=" C GLN A 567 " pdb=" CB GLN A 567 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 1263 not shown) Planarity restraints: 1394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 939 " -0.078 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO A 940 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 940 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 940 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 850 " 0.045 5.00e-02 4.00e+02 6.75e-02 7.28e+00 pdb=" N PRO A 851 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 851 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 851 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 627 " -0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO A 628 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 628 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 628 " -0.035 5.00e-02 4.00e+02 ... (remaining 1391 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 82 2.63 - 3.20: 7370 3.20 - 3.77: 12257 3.77 - 4.33: 16872 4.33 - 4.90: 26779 Nonbonded interactions: 63360 Sorted by model distance: nonbonded pdb=" OD1 ASP A 832 " pdb="MG MG A1201 " model vdw 2.064 2.170 nonbonded pdb=" OD2 ASP A 834 " pdb="MG MG A1201 " model vdw 2.108 2.170 nonbonded pdb=" O LYS A 566 " pdb=" NE2 GLN A 570 " model vdw 2.202 3.120 nonbonded pdb=" O ALA A 432 " pdb=" OG1 THR A 448 " model vdw 2.230 3.040 nonbonded pdb=" NH2 ARG A 633 " pdb=" O LYS A 718 " model vdw 2.288 3.120 ... (remaining 63355 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.680 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.290 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 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 0.088 7895 Z= 0.162 Angle : 0.543 6.992 10712 Z= 0.297 Chirality : 0.042 0.172 1266 Planarity : 0.005 0.115 1394 Dihedral : 13.572 78.881 2763 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: -1.53 (0.26), residues: 1047 helix: 0.52 (0.28), residues: 378 sheet: -2.31 (0.42), residues: 152 loop : -1.78 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 501 HIS 0.004 0.001 HIS A 304 PHE 0.019 0.001 PHE A 251 TYR 0.015 0.001 TYR A 747 ARG 0.008 0.001 ARG A 729 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.6239 (mtmm) cc_final: 0.5837 (mtmm) REVERT: A 311 PHE cc_start: 0.7238 (t80) cc_final: 0.7036 (t80) REVERT: A 331 LEU cc_start: 0.8136 (mm) cc_final: 0.7929 (mt) REVERT: A 864 ASP cc_start: 0.7488 (p0) cc_final: 0.7227 (p0) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2467 time to fit residues: 58.8566 Evaluate side-chains 102 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.4980 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 83 optimal weight: 0.1980 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 0.0040 chunk 61 optimal weight: 0.6980 chunk 96 optimal weight: 7.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS A 538 GLN A 619 ASN A 816 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.111893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.090342 restraints weight = 18174.992| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.55 r_work: 0.3396 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7895 Z= 0.199 Angle : 0.628 11.374 10712 Z= 0.324 Chirality : 0.043 0.157 1266 Planarity : 0.005 0.073 1394 Dihedral : 4.533 22.495 1117 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.79 % Allowed : 10.91 % Favored : 88.30 % 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: -1.30 (0.26), residues: 1047 helix: 0.53 (0.27), residues: 388 sheet: -2.08 (0.44), residues: 141 loop : -1.59 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 501 HIS 0.005 0.001 HIS A 33 PHE 0.021 0.001 PHE A 837 TYR 0.016 0.001 TYR A 799 ARG 0.006 0.001 ARG A 937 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8315 (m-30) cc_final: 0.7927 (p0) REVERT: A 331 LEU cc_start: 0.8802 (mm) cc_final: 0.8256 (mt) REVERT: A 377 ASN cc_start: 0.9106 (t0) cc_final: 0.8899 (t0) REVERT: A 771 GLU cc_start: 0.7879 (pm20) cc_final: 0.7564 (pm20) REVERT: A 864 ASP cc_start: 0.8753 (p0) cc_final: 0.8481 (p0) REVERT: A 923 LYS cc_start: 0.9009 (mttm) cc_final: 0.8601 (tttt) outliers start: 6 outliers final: 2 residues processed: 115 average time/residue: 0.2000 time to fit residues: 31.4889 Evaluate side-chains 92 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 567 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 70 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 0.0050 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS A 538 GLN A 816 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.105835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.083609 restraints weight = 18651.266| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.57 r_work: 0.3259 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7895 Z= 0.389 Angle : 0.676 8.979 10712 Z= 0.349 Chirality : 0.046 0.195 1266 Planarity : 0.005 0.057 1394 Dihedral : 4.836 25.640 1117 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.23 % Allowed : 12.09 % Favored : 85.68 % 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: -1.47 (0.26), residues: 1047 helix: 0.50 (0.26), residues: 391 sheet: -2.32 (0.41), residues: 137 loop : -1.76 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 501 HIS 0.006 0.001 HIS A 822 PHE 0.016 0.002 PHE A 181 TYR 0.015 0.001 TYR A 808 ARG 0.006 0.001 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8391 (m-30) cc_final: 0.8030 (p0) REVERT: A 92 TYR cc_start: 0.6065 (t80) cc_final: 0.5815 (t80) REVERT: A 218 MET cc_start: 0.8277 (ttt) cc_final: 0.8043 (ttm) REVERT: A 331 LEU cc_start: 0.8948 (mm) cc_final: 0.8596 (mm) REVERT: A 738 MET cc_start: 0.9003 (ptp) cc_final: 0.8722 (ptp) REVERT: A 864 ASP cc_start: 0.8731 (p0) cc_final: 0.8527 (p0) REVERT: A 923 LYS cc_start: 0.9034 (mttm) cc_final: 0.8702 (tttt) outliers start: 17 outliers final: 9 residues processed: 96 average time/residue: 0.1897 time to fit residues: 25.7799 Evaluate side-chains 80 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 763 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 56.2764 > 50: distance: 97 - 102: 11.624 distance: 102 - 103: 10.211 distance: 103 - 104: 10.072 distance: 103 - 106: 9.858 distance: 104 - 105: 22.507 distance: 104 - 114: 11.106 distance: 106 - 107: 5.215 distance: 107 - 108: 3.065 distance: 107 - 109: 3.674 distance: 109 - 111: 5.725 distance: 110 - 112: 7.146 distance: 112 - 113: 3.637 distance: 114 - 115: 14.965 distance: 115 - 116: 34.694 distance: 115 - 118: 13.745 distance: 116 - 117: 33.921 distance: 116 - 122: 35.393 distance: 118 - 119: 17.167 distance: 118 - 120: 8.740 distance: 119 - 121: 10.222 distance: 122 - 123: 30.854 distance: 123 - 124: 35.546 distance: 123 - 126: 26.424 distance: 124 - 125: 23.682 distance: 124 - 128: 21.745 distance: 126 - 127: 15.375 distance: 128 - 129: 41.314 distance: 129 - 130: 36.755 distance: 129 - 132: 56.276 distance: 130 - 131: 17.944 distance: 130 - 137: 20.720 distance: 132 - 133: 22.735 distance: 133 - 134: 33.641 distance: 134 - 135: 27.747 distance: 134 - 136: 25.561 distance: 137 - 138: 49.220 distance: 138 - 139: 21.669 distance: 138 - 141: 30.077 distance: 139 - 140: 22.489 distance: 139 - 143: 11.210 distance: 141 - 142: 24.091 distance: 143 - 144: 12.971 distance: 144 - 145: 19.743 distance: 144 - 147: 14.455 distance: 145 - 146: 10.806 distance: 145 - 150: 16.837 distance: 147 - 148: 13.717 distance: 147 - 149: 13.577 distance: 150 - 151: 16.186 distance: 151 - 152: 9.310 distance: 151 - 154: 14.640 distance: 152 - 153: 18.496 distance: 152 - 161: 9.159 distance: 154 - 155: 8.257 distance: 155 - 156: 8.516 distance: 155 - 157: 7.937 distance: 156 - 158: 5.662 distance: 157 - 159: 4.065 distance: 158 - 160: 4.298 distance: 159 - 160: 6.055 distance: 161 - 162: 14.255 distance: 162 - 163: 23.368 distance: 163 - 164: 10.805 distance: 163 - 165: 16.342 distance: 165 - 166: 11.522 distance: 166 - 167: 8.423 distance: 166 - 169: 21.484 distance: 167 - 168: 10.142 distance: 167 - 174: 10.699 distance: 168 - 198: 7.168 distance: 169 - 170: 14.432 distance: 170 - 171: 6.801 distance: 171 - 172: 10.319 distance: 172 - 173: 6.972 distance: 174 - 175: 11.883 distance: 175 - 176: 8.877 distance: 175 - 178: 7.154 distance: 176 - 177: 5.565 distance: 176 - 182: 5.857 distance: 177 - 203: 4.630 distance: 178 - 179: 5.057 distance: 179 - 180: 5.421