Starting phenix.real_space_refine on Thu Mar 6 00:01:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wr7_32717/03_2025/7wr7_32717.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wr7_32717/03_2025/7wr7_32717.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/7wr7_32717/03_2025/7wr7_32717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wr7_32717/03_2025/7wr7_32717.map" model { file = "/net/cci-nas-00/data/ceres_data/7wr7_32717/03_2025/7wr7_32717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wr7_32717/03_2025/7wr7_32717.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= -0.001 sd= 0.054 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 34 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: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 2509 2.51 5 N 681 2.21 5 O 776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3995 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2013 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 15, 'TRANS': 245} Chain: "B" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1844 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 220} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 68 Unusual residues: {'GBS': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GBS:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.33, per 1000 atoms: 0.83 Number of scatterers: 3995 At special positions: 0 Unit cell: (64.852, 80.542, 95.186, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 776 8.00 N 681 7.00 C 2509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 677 " distance=2.03 Simple disulfide: pdb=" SG CYS A 716 " - pdb=" SG CYS A 767 " distance=2.03 Simple disulfide: pdb=" SG CYS A 772 " - pdb=" SG CYS B 896 " distance=2.03 Simple disulfide: pdb=" SG CYS B 810 " - pdb=" SG CYS B 826 " distance=2.03 Simple disulfide: pdb=" SG CYS B 910 " - pdb=" SG CYS B 977 " distance=2.03 Simple disulfide: pdb=" SG CYS B 941 " - pdb=" SG CYS B 956 " distance=2.03 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS B 995 " 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=1, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 534 " " NAG A 802 " - " ASN A 630 " " NAG A 803 " - " ASN A 682 " " NAG A 804 " - " ASN A 706 " " NAG A 805 " - " ASN A 725 " " NAG B1101 " - " ASN B 848 " " NAG B1102 " - " ASN B 887 " " NAG B1103 " - " ASN B 909 " " NAG B1104 " - " ASN B 949 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 477.5 milliseconds 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 904 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 7 sheets defined 7.9% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 671 through 675 Processing helix chain 'A' and resid 708 through 719 Processing helix chain 'B' and resid 833 through 835 No H-bonds generated for 'chain 'B' and resid 833 through 835' Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 1010 through 1019 removed outlier: 4.071A pdb=" N PHE B1017 " --> pdb=" O TRP B1013 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS B1019 " --> pdb=" O GLN B1015 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 538 removed outlier: 3.744A pdb=" N PHE A 537 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 629 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 572 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN A 630 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N PHE A 568 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR A 632 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU A 566 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY A 634 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE A 564 " --> pdb=" O GLY A 634 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 551 through 557 removed outlier: 3.757A pdb=" N CYS A 552 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 594 " --> pdb=" O ILE A 582 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 693 through 694 Processing sheet with id=AA4, first strand: chain 'A' and resid 728 through 729 removed outlier: 3.899A pdb=" N LYS A 728 " --> pdb=" O ARG A 764 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 740 through 741 removed outlier: 3.705A pdb=" N THR A 752 " --> pdb=" O LYS A 740 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 789 through 790 removed outlier: 3.856A pdb=" N GLN B 929 " --> pdb=" O GLY B 914 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 914 " --> pdb=" O GLN B 929 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ASN B 909 " --> pdb=" O GLN B 978 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLN B 978 " --> pdb=" O ASN B 909 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA B 913 " --> pdb=" O PRO B 974 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU B 975 " --> pdb=" O ALA B 986 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS B 977 " --> pdb=" O PHE B 984 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL B1003 " --> pdb=" O SER B 990 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 820 through 821 removed outlier: 5.813A pdb=" N LEU B 808 " --> pdb=" O TYR B 804 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR B 804 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N CYS B 810 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 802 " --> pdb=" O CYS B 810 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N TRP B 837 " --> pdb=" O ILE B 859 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU B 861 " --> pdb=" O HIS B 881 " (cutoff:3.500A) 77 hydrogen bonds defined for protein. 198 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: 1.09 Time building geometry restraints manager: 1.25 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: 1015 1.33 - 1.45: 823 1.45 - 1.57: 2218 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 4092 Sorted by residual: bond pdb=" C18 GBS B1105 " pdb=" N3 GBS B1105 " ideal model delta sigma weight residual 1.387 1.333 0.054 2.00e-02 2.50e+03 7.17e+00 bond pdb=" N GLN B 968 " pdb=" CA GLN B 968 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.25e-02 6.40e+03 6.52e+00 bond pdb=" O GBS B1105 " pdb=" C6 GBS B1105 " ideal model delta sigma weight residual 1.260 1.210 0.050 2.00e-02 2.50e+03 6.17e+00 bond pdb=" N SER B 971 " pdb=" CA SER B 971 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.23e-02 6.61e+03 6.15e+00 bond pdb=" N GLY B 973 " pdb=" CA GLY B 973 " ideal model delta sigma weight residual 1.443 1.476 -0.033 1.37e-02 5.33e+03 5.83e+00 ... (remaining 4087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 5343 1.40 - 2.81: 185 2.81 - 4.21: 31 4.21 - 5.62: 5 5.62 - 7.02: 5 Bond angle restraints: 5569 Sorted by residual: angle pdb=" N ASP B 970 " pdb=" CA ASP B 970 " pdb=" C ASP B 970 " ideal model delta sigma weight residual 114.56 108.41 6.15 1.27e+00 6.20e-01 2.35e+01 angle pdb=" N PRO B 974 " pdb=" CA PRO B 974 " pdb=" CB PRO B 974 " ideal model delta sigma weight residual 103.25 98.83 4.42 1.05e+00 9.07e-01 1.77e+01 angle pdb=" CA GLN B 968 " pdb=" C GLN B 968 " pdb=" O GLN B 968 " ideal model delta sigma weight residual 121.55 118.32 3.23 1.06e+00 8.90e-01 9.31e+00 angle pdb=" N GLY B 972 " pdb=" CA GLY B 972 " pdb=" C GLY B 972 " ideal model delta sigma weight residual 115.32 111.24 4.08 1.38e+00 5.25e-01 8.75e+00 angle pdb=" N PHE A 542 " pdb=" CA PHE A 542 " pdb=" C PHE A 542 " ideal model delta sigma weight residual 109.81 115.70 -5.89 2.21e+00 2.05e-01 7.10e+00 ... (remaining 5564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.22: 2391 16.22 - 32.45: 115 32.45 - 48.67: 30 48.67 - 64.89: 9 64.89 - 81.12: 1 Dihedral angle restraints: 2546 sinusoidal: 1134 harmonic: 1412 Sorted by residual: dihedral pdb=" CA PRO A 543 " pdb=" C PRO A 543 " pdb=" N ASN A 544 " pdb=" CA ASN A 544 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CB CYS A 772 " pdb=" SG CYS A 772 " pdb=" SG CYS B 896 " pdb=" CB CYS B 896 " ideal model delta sinusoidal sigma weight residual -86.00 -113.70 27.70 1 1.00e+01 1.00e-02 1.10e+01 dihedral pdb=" CA SER A 539 " pdb=" C SER A 539 " pdb=" N THR A 540 " pdb=" CA THR A 540 " ideal model delta harmonic sigma weight residual 180.00 163.44 16.56 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 2543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 404 0.033 - 0.067: 140 0.067 - 0.100: 55 0.100 - 0.134: 28 0.134 - 0.167: 1 Chirality restraints: 628 Sorted by residual: chirality pdb=" C2 NAG A 804 " pdb=" C1 NAG A 804 " pdb=" C3 NAG A 804 " pdb=" N2 NAG A 804 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CA VAL B 988 " pdb=" N VAL B 988 " pdb=" C VAL B 988 " pdb=" CB VAL B 988 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CB VAL A 691 " pdb=" CA VAL A 691 " pdb=" CG1 VAL A 691 " pdb=" CG2 VAL A 691 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.71e-01 ... (remaining 625 not shown) Planarity restraints: 733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 GBS B1105 " 0.013 2.00e-02 2.50e+03 3.50e-02 1.53e+01 pdb=" C2 GBS B1105 " -0.041 2.00e-02 2.50e+03 pdb=" N2 GBS B1105 " 0.055 2.00e-02 2.50e+03 pdb=" N3 GBS B1105 " -0.034 2.00e-02 2.50e+03 pdb=" N4 GBS B1105 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GBS B1105 " -0.026 2.00e-02 2.50e+03 2.49e-02 1.24e+01 pdb=" C1 GBS B1105 " 0.009 2.00e-02 2.50e+03 pdb=" C2 GBS B1105 " 0.028 2.00e-02 2.50e+03 pdb=" C3 GBS B1105 " 0.008 2.00e-02 2.50e+03 pdb=" C4 GBS B1105 " -0.026 2.00e-02 2.50e+03 pdb=" C5 GBS B1105 " -0.031 2.00e-02 2.50e+03 pdb=" C6 GBS B1105 " 0.041 2.00e-02 2.50e+03 pdb=" N2 GBS B1105 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 532 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO A 533 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 533 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 533 " -0.022 5.00e-02 4.00e+02 ... (remaining 730 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1243 2.83 - 3.35: 3694 3.35 - 3.86: 6398 3.86 - 4.38: 7329 4.38 - 4.90: 12603 Nonbonded interactions: 31267 Sorted by model distance: nonbonded pdb=" OD2 ASP B 874 " pdb=" ND2 ASN B 875 " model vdw 2.309 3.120 nonbonded pdb=" NH2 ARG B 908 " pdb=" O GLN B 978 " model vdw 2.350 3.120 nonbonded pdb=" O GLY B 811 " pdb=" O GLY B 972 " model vdw 2.357 3.040 nonbonded pdb=" NZ LYS A 740 " pdb=" O SER A 754 " model vdw 2.359 3.120 nonbonded pdb=" O CYS B 826 " pdb=" NH1 ARG B 830 " model vdw 2.367 3.120 ... (remaining 31262 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: 11.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.020 Find NCS groups from input model: 0.050 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 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 : 0.004 0.054 4092 Z= 0.219 Angle : 0.607 7.023 5569 Z= 0.331 Chirality : 0.044 0.167 628 Planarity : 0.003 0.039 724 Dihedral : 10.283 81.116 1618 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 3.29 % Allowed : 6.59 % Favored : 90.12 % 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: -4.53 (0.30), residues: 492 helix: -2.64 (0.51), residues: 36 sheet: -2.64 (0.42), residues: 105 loop : -3.42 (0.28), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 699 HIS 0.002 0.000 HIS B 825 PHE 0.005 0.001 PHE A 627 TYR 0.004 0.001 TYR A 546 ARG 0.001 0.000 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 ARG cc_start: 0.8346 (ptp-170) cc_final: 0.7770 (mtm110) REVERT: A 707 TRP cc_start: 0.8525 (t-100) cc_final: 0.7932 (t-100) REVERT: B 959 TYR cc_start: 0.8034 (m-80) cc_final: 0.7809 (m-10) outliers start: 14 outliers final: 5 residues processed: 121 average time/residue: 0.2318 time to fit residues: 32.6980 Evaluate side-chains 77 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 660 ASN Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 896 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 20 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 649 GLN A 713 ASN A 717 GLN ** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 GLN B 938 ASN B 943 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.168899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.119393 restraints weight = 5064.345| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 3.35 r_work: 0.3607 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4092 Z= 0.250 Angle : 0.614 9.545 5569 Z= 0.310 Chirality : 0.047 0.245 628 Planarity : 0.004 0.045 724 Dihedral : 7.568 55.607 728 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 3.06 % Allowed : 13.41 % Favored : 83.53 % 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: -3.88 (0.34), residues: 492 helix: -1.94 (0.69), residues: 38 sheet: -2.30 (0.38), residues: 127 loop : -2.94 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1013 HIS 0.005 0.001 HIS A 665 PHE 0.010 0.001 PHE A 542 TYR 0.007 0.001 TYR B 920 ARG 0.004 0.001 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 707 TRP cc_start: 0.8689 (t-100) cc_final: 0.8005 (t-100) REVERT: B 803 TYR cc_start: 0.8465 (m-80) cc_final: 0.7883 (m-80) REVERT: B 859 ILE cc_start: 0.8325 (mm) cc_final: 0.7943 (mm) REVERT: B 954 MET cc_start: 0.7451 (mtt) cc_final: 0.7213 (mtm) REVERT: B 1017 PHE cc_start: 0.7540 (m-10) cc_final: 0.7271 (m-10) outliers start: 13 outliers final: 6 residues processed: 80 average time/residue: 0.2599 time to fit residues: 24.6799 Evaluate side-chains 73 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 911 SER Chi-restraints excluded: chain B residue 938 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 13 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 660 ASN B 844 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.177606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.127980 restraints weight = 5212.628| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 3.67 r_work: 0.3577 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4092 Z= 0.225 Angle : 0.583 9.404 5569 Z= 0.292 Chirality : 0.046 0.241 628 Planarity : 0.004 0.053 724 Dihedral : 6.978 55.855 721 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 2.82 % Allowed : 13.88 % Favored : 83.29 % 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: -3.60 (0.34), residues: 492 helix: -1.44 (0.74), residues: 38 sheet: -2.04 (0.39), residues: 127 loop : -2.83 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 798 HIS 0.004 0.001 HIS A 665 PHE 0.009 0.001 PHE A 627 TYR 0.007 0.001 TYR B 920 ARG 0.003 0.001 ARG A 692 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 540 THR cc_start: 0.8062 (OUTLIER) cc_final: 0.7836 (p) REVERT: A 679 ARG cc_start: 0.8731 (ptp-170) cc_final: 0.8226 (mtm110) REVERT: A 717 GLN cc_start: 0.8868 (pp30) cc_final: 0.8646 (pp30) REVERT: A 766 GLN cc_start: 0.7254 (mm-40) cc_final: 0.6957 (mm-40) REVERT: B 803 TYR cc_start: 0.8476 (m-80) cc_final: 0.7781 (m-80) REVERT: B 859 ILE cc_start: 0.8350 (mm) cc_final: 0.7992 (mm) outliers start: 12 outliers final: 9 residues processed: 75 average time/residue: 0.2028 time to fit residues: 19.2190 Evaluate side-chains 72 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 635 TYR Chi-restraints excluded: chain A residue 660 ASN Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 911 SER Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 0.0570 overall best weight: 0.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN A 660 ASN B 938 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.176479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.126241 restraints weight = 5275.134| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 3.68 r_work: 0.3536 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4092 Z= 0.254 Angle : 0.589 9.381 5569 Z= 0.300 Chirality : 0.046 0.236 628 Planarity : 0.004 0.047 724 Dihedral : 6.964 55.819 721 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 2.82 % Allowed : 15.53 % Favored : 81.65 % 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: -3.37 (0.35), residues: 492 helix: -1.11 (0.79), residues: 38 sheet: -1.89 (0.40), residues: 138 loop : -2.68 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 798 HIS 0.004 0.001 HIS A 567 PHE 0.009 0.001 PHE A 627 TYR 0.007 0.001 TYR B1004 ARG 0.005 0.001 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 ARG cc_start: 0.8729 (ptp-170) cc_final: 0.8474 (ptp-170) REVERT: A 717 GLN cc_start: 0.8912 (pp30) cc_final: 0.8657 (pp30) REVERT: A 766 GLN cc_start: 0.7313 (mm-40) cc_final: 0.7033 (mm-40) REVERT: B 803 TYR cc_start: 0.8566 (m-80) cc_final: 0.7687 (m-80) REVERT: B 859 ILE cc_start: 0.8329 (mm) cc_final: 0.7975 (mm) outliers start: 12 outliers final: 7 residues processed: 75 average time/residue: 0.3881 time to fit residues: 36.0597 Evaluate side-chains 64 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 911 SER Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 0.0870 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 ASN B 978 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.174511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.124944 restraints weight = 5375.362| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 3.67 r_work: 0.3520 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4092 Z= 0.246 Angle : 0.587 9.363 5569 Z= 0.298 Chirality : 0.046 0.232 628 Planarity : 0.005 0.060 724 Dihedral : 6.923 56.987 720 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 2.82 % Allowed : 16.47 % Favored : 80.71 % 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: -3.20 (0.36), residues: 492 helix: -0.82 (0.84), residues: 38 sheet: -1.75 (0.41), residues: 138 loop : -2.60 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 798 HIS 0.003 0.001 HIS A 567 PHE 0.014 0.001 PHE A 542 TYR 0.009 0.001 TYR B 920 ARG 0.005 0.001 ARG A 692 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7590 (tp) cc_final: 0.7133 (tt) REVERT: A 565 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: A 679 ARG cc_start: 0.8747 (ptp-170) cc_final: 0.8481 (ptp-170) REVERT: A 717 GLN cc_start: 0.8946 (pp30) cc_final: 0.8658 (pp30) REVERT: A 766 GLN cc_start: 0.7497 (mm-40) cc_final: 0.7135 (mm-40) REVERT: B 803 TYR cc_start: 0.8625 (m-80) cc_final: 0.7614 (m-80) REVERT: B 859 ILE cc_start: 0.8317 (mm) cc_final: 0.7967 (mm) outliers start: 12 outliers final: 8 residues processed: 69 average time/residue: 0.1595 time to fit residues: 13.8053 Evaluate side-chains 68 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 635 TYR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 938 ASN Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 26 optimal weight: 0.0030 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.157787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.108791 restraints weight = 5304.388| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 3.46 r_work: 0.3512 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4092 Z= 0.241 Angle : 0.580 9.362 5569 Z= 0.295 Chirality : 0.046 0.231 628 Planarity : 0.004 0.046 724 Dihedral : 6.867 57.713 720 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 3.29 % Allowed : 15.76 % Favored : 80.94 % 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: -3.09 (0.36), residues: 492 helix: -0.78 (0.84), residues: 38 sheet: -1.69 (0.41), residues: 138 loop : -2.52 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 798 HIS 0.003 0.001 HIS A 567 PHE 0.014 0.001 PHE A 681 TYR 0.008 0.001 TYR B 920 ARG 0.007 0.001 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7630 (tp) cc_final: 0.7188 (tt) REVERT: A 565 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7939 (tm-30) REVERT: A 679 ARG cc_start: 0.8714 (ptp-170) cc_final: 0.8445 (ptp-170) REVERT: A 707 TRP cc_start: 0.8620 (t-100) cc_final: 0.8383 (t-100) REVERT: A 717 GLN cc_start: 0.8978 (pp30) cc_final: 0.8661 (pp30) REVERT: B 803 TYR cc_start: 0.8649 (m-80) cc_final: 0.7625 (m-80) REVERT: B 859 ILE cc_start: 0.8342 (mm) cc_final: 0.7992 (mm) outliers start: 14 outliers final: 11 residues processed: 69 average time/residue: 0.1869 time to fit residues: 16.5226 Evaluate side-chains 67 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 635 TYR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 938 ASN Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 4 optimal weight: 0.4980 chunk 13 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 ASN B 938 ASN B 978 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.158262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.109911 restraints weight = 5321.271| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 3.43 r_work: 0.3501 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4092 Z= 0.218 Angle : 0.583 9.395 5569 Z= 0.296 Chirality : 0.046 0.231 628 Planarity : 0.005 0.067 724 Dihedral : 6.796 57.881 720 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 1.88 % Allowed : 17.41 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.37), residues: 492 helix: -0.71 (0.85), residues: 38 sheet: -1.50 (0.42), residues: 130 loop : -2.43 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 798 HIS 0.003 0.001 HIS A 567 PHE 0.018 0.001 PHE A 681 TYR 0.009 0.001 TYR B 920 ARG 0.005 0.000 ARG A 692 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7653 (tp) cc_final: 0.7237 (tt) REVERT: A 679 ARG cc_start: 0.8687 (ptp-170) cc_final: 0.8437 (ptp-170) REVERT: A 707 TRP cc_start: 0.8558 (t-100) cc_final: 0.8309 (t-100) REVERT: A 766 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7383 (mm-40) REVERT: B 803 TYR cc_start: 0.8669 (m-80) cc_final: 0.7602 (m-80) REVERT: B 859 ILE cc_start: 0.8328 (mm) cc_final: 0.7976 (mm) outliers start: 8 outliers final: 7 residues processed: 65 average time/residue: 0.1624 time to fit residues: 13.3509 Evaluate side-chains 64 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 938 ASN Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 0.0270 chunk 17 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.150072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.106136 restraints weight = 5115.693| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.31 r_work: 0.3331 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4092 Z= 0.197 Angle : 0.578 9.399 5569 Z= 0.293 Chirality : 0.046 0.230 628 Planarity : 0.004 0.046 724 Dihedral : 6.747 57.881 720 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer: Outliers : 2.35 % Allowed : 17.41 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.37), residues: 492 helix: -0.78 (0.83), residues: 38 sheet: -1.39 (0.43), residues: 130 loop : -2.39 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 798 HIS 0.003 0.000 HIS A 567 PHE 0.018 0.001 PHE A 681 TYR 0.009 0.001 TYR B 920 ARG 0.008 0.000 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7607 (tp) cc_final: 0.7211 (tt) REVERT: A 565 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8050 (tm-30) REVERT: A 679 ARG cc_start: 0.8654 (ptp-170) cc_final: 0.8407 (ptp-170) REVERT: A 692 ARG cc_start: 0.8137 (ttm170) cc_final: 0.7909 (ttm-80) REVERT: A 707 TRP cc_start: 0.8549 (t-100) cc_final: 0.8324 (t-100) REVERT: A 717 GLN cc_start: 0.8995 (pp30) cc_final: 0.8674 (pp30) REVERT: B 803 TYR cc_start: 0.8687 (m-80) cc_final: 0.7641 (m-80) REVERT: B 859 ILE cc_start: 0.8333 (mm) cc_final: 0.7984 (mm) outliers start: 10 outliers final: 8 residues processed: 64 average time/residue: 0.1562 time to fit residues: 12.6248 Evaluate side-chains 62 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 938 ASN Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 0.0000 chunk 25 optimal weight: 0.9980 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 ASN B 978 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.149428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.101061 restraints weight = 5403.190| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.58 r_work: 0.3269 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4092 Z= 0.325 Angle : 0.612 9.288 5569 Z= 0.313 Chirality : 0.047 0.229 628 Planarity : 0.004 0.045 724 Dihedral : 6.837 58.075 720 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.80 % Favored : 87.20 % Rotamer: Outliers : 2.59 % Allowed : 16.71 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.37), residues: 492 helix: -0.71 (0.83), residues: 38 sheet: -1.56 (0.42), residues: 130 loop : -2.42 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 798 HIS 0.006 0.001 HIS A 567 PHE 0.016 0.002 PHE A 681 TYR 0.009 0.001 TYR B 920 ARG 0.003 0.000 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7832 (tp) cc_final: 0.7395 (tt) REVERT: A 679 ARG cc_start: 0.8655 (ptp-170) cc_final: 0.8416 (ptp-170) REVERT: A 692 ARG cc_start: 0.8160 (ttm170) cc_final: 0.7936 (ttm-80) REVERT: A 707 TRP cc_start: 0.8580 (t-100) cc_final: 0.8347 (t-100) REVERT: A 766 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7462 (mm-40) REVERT: B 803 TYR cc_start: 0.8784 (m-80) cc_final: 0.7706 (m-80) REVERT: B 859 ILE cc_start: 0.8415 (mm) cc_final: 0.8071 (mm) outliers start: 11 outliers final: 8 residues processed: 68 average time/residue: 0.1596 time to fit residues: 13.6246 Evaluate side-chains 67 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 938 ASN Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 67.9812 > 50: distance: 24 - 29: 18.554 distance: 29 - 30: 41.748 distance: 29 - 35: 9.930 distance: 30 - 31: 41.853 distance: 30 - 33: 31.773 distance: 31 - 32: 21.423 distance: 31 - 36: 15.046 distance: 33 - 34: 18.676 distance: 34 - 35: 21.558 distance: 36 - 37: 16.983 distance: 37 - 38: 22.760 distance: 37 - 40: 19.933 distance: 38 - 39: 18.704 distance: 38 - 44: 12.055 distance: 40 - 41: 14.422 distance: 41 - 42: 8.309 distance: 41 - 43: 5.680 distance: 44 - 45: 31.791 distance: 45 - 46: 49.231 distance: 45 - 48: 26.483 distance: 46 - 47: 34.860 distance: 46 - 50: 25.839 distance: 48 - 49: 13.917 distance: 50 - 51: 22.004 distance: 51 - 52: 45.149 distance: 51 - 54: 46.146 distance: 52 - 53: 29.268 distance: 52 - 62: 35.431 distance: 54 - 55: 32.873 distance: 55 - 56: 11.994 distance: 55 - 57: 18.706 distance: 56 - 58: 6.950 distance: 57 - 59: 7.375 distance: 58 - 60: 5.363 distance: 59 - 60: 3.213 distance: 60 - 61: 3.840 distance: 62 - 63: 37.755 distance: 62 - 68: 10.334 distance: 63 - 64: 36.405 distance: 63 - 66: 27.392 distance: 64 - 65: 24.793 distance: 64 - 69: 39.394 distance: 66 - 67: 20.392 distance: 67 - 68: 23.183 distance: 69 - 70: 50.257 distance: 70 - 71: 35.283 distance: 70 - 73: 60.424 distance: 71 - 72: 23.289 distance: 71 - 77: 17.516 distance: 73 - 74: 67.981 distance: 74 - 75: 55.133 distance: 74 - 76: 38.877 distance: 77 - 78: 34.496 distance: 78 - 79: 36.459 distance: 78 - 81: 38.025 distance: 79 - 80: 30.868 distance: 79 - 85: 39.272 distance: 81 - 82: 15.534 distance: 82 - 83: 15.102 distance: 82 - 84: 9.682 distance: 85 - 86: 41.574 distance: 86 - 87: 34.989 distance: 86 - 89: 27.383 distance: 87 - 88: 44.279 distance: 87 - 90: 35.882 distance: 90 - 91: 29.936 distance: 91 - 92: 32.574 distance: 91 - 94: 24.499 distance: 92 - 93: 19.701 distance: 92 - 101: 32.415 distance: 94 - 95: 10.497 distance: 95 - 96: 10.702 distance: 95 - 97: 4.451 distance: 96 - 98: 6.586 distance: 97 - 99: 7.480 distance: 98 - 100: 17.105 distance: 99 - 100: 16.923 distance: 101 - 102: 39.260 distance: 102 - 103: 22.519 distance: 102 - 105: 23.950 distance: 103 - 104: 16.715 distance: 103 - 107: 15.154 distance: 104 - 145: 16.182 distance: 105 - 106: 11.749