Starting phenix.real_space_refine on Tue Jan 14 19:48:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wvy_37876/01_2025/8wvy_37876.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wvy_37876/01_2025/8wvy_37876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wvy_37876/01_2025/8wvy_37876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wvy_37876/01_2025/8wvy_37876.map" model { file = "/net/cci-nas-00/data/ceres_data/8wvy_37876/01_2025/8wvy_37876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wvy_37876/01_2025/8wvy_37876.cif" } resolution = 3.29 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= 0.004 sd= 0.027 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 4642 2.51 5 N 1237 2.21 5 O 1305 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-5571/modules/chem_data/mon_lib" Total number of atoms: 7241 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5671 Classifications: {'peptide': 731} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 36, 'TRANS': 694} Chain breaks: 4 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 788 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "F" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 782 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Time building chain proxies: 5.27, per 1000 atoms: 0.73 Number of scatterers: 7241 At special positions: 0 Unit cell: (146.2, 111.35, 126.65, 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 57 16.00 O 1305 8.00 N 1237 7.00 C 4642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 35 " distance=2.11 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 43 " distance=2.14 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 364 " distance=2.05 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 522 " distance=1.89 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 532 " distance=2.14 Simple disulfide: pdb=" SG CYS A 618 " - pdb=" SG CYS A 693 " distance=2.00 Simple disulfide: pdb=" SG CYS E 39 " - pdb=" SG CYS E 96 " distance=2.00 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 110 " distance=1.72 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 126 " distance=2.07 Simple disulfide: pdb=" SG CYS E 69 " - pdb=" SG CYS E 128 " distance=1.99 Simple disulfide: pdb=" SG CYS E 93 " - pdb=" SG CYS F 95 " distance=2.07 Simple disulfide: pdb=" SG CYS E 95 " - pdb=" SG CYS F 93 " distance=2.14 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS F 131 " distance=1.87 Simple disulfide: pdb=" SG CYS F 39 " - pdb=" SG CYS F 96 " distance=2.12 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 110 " distance=2.48 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 126 " distance=1.77 Simple disulfide: pdb=" SG CYS F 69 " - pdb=" SG CYS F 128 " distance=2.34 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 919.9 milliseconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 11 sheets defined 26.0% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.747A pdb=" N GLN A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 469 through 474 removed outlier: 4.202A pdb=" N PHE A 473 " --> pdb=" O GLN A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 564 removed outlier: 3.728A pdb=" N LEU A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 601 removed outlier: 4.147A pdb=" N ILE A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'A' and resid 616 through 647 removed outlier: 3.735A pdb=" N ILE A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 679 removed outlier: 3.688A pdb=" N PHE A 662 " --> pdb=" O HIS A 658 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 682 No H-bonds generated for 'chain 'A' and resid 680 through 682' Processing helix chain 'A' and resid 705 through 731 Processing helix chain 'A' and resid 741 through 768 removed outlier: 3.620A pdb=" N LEU A 752 " --> pdb=" O HIS A 748 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS A 757 " --> pdb=" O ILE A 753 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 758 " --> pdb=" O PHE A 754 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N PHE A 759 " --> pdb=" O THR A 755 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A 760 " --> pdb=" O ASN A 756 " (cutoff:3.500A) Proline residue: A 762 - end of helix Processing helix chain 'A' and resid 768 through 773 removed outlier: 4.302A pdb=" N ILE A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 776 No H-bonds generated for 'chain 'A' and resid 774 through 776' Processing helix chain 'A' and resid 778 through 790 Processing helix chain 'A' and resid 792 through 803 removed outlier: 3.504A pdb=" N LEU A 796 " --> pdb=" O LEU A 792 " (cutoff:3.500A) Proline residue: A 798 - end of helix removed outlier: 3.995A pdb=" N TYR A 801 " --> pdb=" O ASN A 797 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 803 " --> pdb=" O VAL A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 820 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.637A pdb=" N THR A 183 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU A 182 " --> pdb=" O HIS A 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192 removed outlier: 3.664A pdb=" N ILE A 192 " --> pdb=" O SER A 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 262 through 263 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 304 removed outlier: 6.880A pdb=" N LEU A 348 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A 394 " --> pdb=" O ASP A 419 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU A 418 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA7, first strand: chain 'E' and resid 40 through 48 removed outlier: 8.437A pdb=" N ALA E 63 " --> pdb=" O PRO F 77 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS E 65 " --> pdb=" O SER F 75 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER F 73 " --> pdb=" O GLY E 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 89 through 92 removed outlier: 3.679A pdb=" N SER E 73 " --> pdb=" O GLY F 67 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY F 67 " --> pdb=" O SER E 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER E 75 " --> pdb=" O CYS F 65 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ALA F 63 " --> pdb=" O PRO E 77 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL F 60 " --> pdb=" O ASP F 46 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP F 46 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR F 44 " --> pdb=" O LEU F 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 94 through 107 removed outlier: 6.279A pdb=" N HIS E 94 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLU E 130 " --> pdb=" O HIS E 94 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N CYS E 96 " --> pdb=" O CYS E 128 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS E 128 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N CYS E 126 " --> pdb=" O PRO E 98 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR E 100 " --> pdb=" O LEU E 124 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 94 through 100 removed outlier: 6.822A pdb=" N SER F 125 " --> pdb=" O GLN F 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 103 through 104 removed outlier: 3.622A pdb=" N TYR F 120 " --> pdb=" O LYS F 104 " (cutoff:3.500A) 223 hydrogen bonds defined for protein. 651 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: 2.29 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1481 1.32 - 1.45: 1671 1.45 - 1.57: 4184 1.57 - 1.69: 0 1.69 - 1.82: 72 Bond restraints: 7408 Sorted by residual: bond pdb=" C THR F 100 " pdb=" N SER F 101 " ideal model delta sigma weight residual 1.331 1.560 -0.228 1.30e-02 5.92e+03 3.08e+02 bond pdb=" C PRO A 770 " pdb=" N LEU A 771 " ideal model delta sigma weight residual 1.334 1.519 -0.185 1.33e-02 5.65e+03 1.93e+02 bond pdb=" C LEU A 815 " pdb=" N LYS A 816 " ideal model delta sigma weight residual 1.334 1.488 -0.153 1.27e-02 6.20e+03 1.46e+02 bond pdb=" C PHE A 706 " pdb=" N THR A 707 " ideal model delta sigma weight residual 1.334 1.476 -0.142 1.23e-02 6.61e+03 1.33e+02 bond pdb=" C VAL A 819 " pdb=" N THR A 820 " ideal model delta sigma weight residual 1.329 1.467 -0.138 1.40e-02 5.10e+03 9.71e+01 ... (remaining 7403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.07: 9847 4.07 - 8.13: 159 8.13 - 12.20: 33 12.20 - 16.27: 8 16.27 - 20.33: 3 Bond angle restraints: 10050 Sorted by residual: angle pdb=" O SER F 56 " pdb=" C SER F 56 " pdb=" N SER F 57 " ideal model delta sigma weight residual 121.74 101.48 20.26 1.31e+00 5.83e-01 2.39e+02 angle pdb=" O HIS F 42 " pdb=" C HIS F 42 " pdb=" N HIS F 43 " ideal model delta sigma weight residual 122.43 106.20 16.23 1.26e+00 6.30e-01 1.66e+02 angle pdb=" CA SER F 56 " pdb=" C SER F 56 " pdb=" N SER F 57 " ideal model delta sigma weight residual 116.50 136.83 -20.33 1.63e+00 3.76e-01 1.56e+02 angle pdb=" C SER F 56 " pdb=" N SER F 57 " pdb=" CA SER F 57 " ideal model delta sigma weight residual 122.73 142.51 -19.78 1.62e+00 3.81e-01 1.49e+02 angle pdb=" O THR A 726 " pdb=" C THR A 726 " pdb=" N LYS A 727 " ideal model delta sigma weight residual 122.15 135.44 -13.29 1.14e+00 7.69e-01 1.36e+02 ... (remaining 10045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.99: 4154 11.99 - 23.99: 222 23.99 - 35.98: 76 35.98 - 47.98: 31 47.98 - 59.97: 5 Dihedral angle restraints: 4488 sinusoidal: 1777 harmonic: 2711 Sorted by residual: dihedral pdb=" CB CYS A 29 " pdb=" SG CYS A 29 " pdb=" SG CYS A 35 " pdb=" CB CYS A 35 " ideal model delta sinusoidal sigma weight residual -86.00 -121.47 35.47 1 1.00e+01 1.00e-02 1.78e+01 dihedral pdb=" CA HIS A 683 " pdb=" C HIS A 683 " pdb=" N ARG A 684 " pdb=" CA ARG A 684 " ideal model delta harmonic sigma weight residual -180.00 -163.39 -16.61 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" C HIS A 683 " pdb=" N HIS A 683 " pdb=" CA HIS A 683 " pdb=" CB HIS A 683 " ideal model delta harmonic sigma weight residual -122.60 -114.31 -8.29 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 4485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1003 0.065 - 0.130: 141 0.130 - 0.195: 15 0.195 - 0.260: 6 0.260 - 0.325: 1 Chirality restraints: 1166 Sorted by residual: chirality pdb=" CA HIS A 683 " pdb=" N HIS A 683 " pdb=" C HIS A 683 " pdb=" CB HIS A 683 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA LEU F 108 " pdb=" N LEU F 108 " pdb=" C LEU F 108 " pdb=" CB LEU F 108 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA LEU F 106 " pdb=" N LEU F 106 " pdb=" C LEU F 106 " pdb=" CB LEU F 106 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 1163 not shown) Planarity restraints: 1271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 45 " 0.025 2.00e-02 2.50e+03 5.92e-02 3.51e+01 pdb=" C VAL F 45 " -0.102 2.00e-02 2.50e+03 pdb=" O VAL F 45 " 0.042 2.00e-02 2.50e+03 pdb=" N ASP F 46 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS F 50 " 0.023 2.00e-02 2.50e+03 4.60e-02 2.11e+01 pdb=" C HIS F 50 " -0.080 2.00e-02 2.50e+03 pdb=" O HIS F 50 " 0.030 2.00e-02 2.50e+03 pdb=" N PRO F 51 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 768 " 0.023 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C PHE A 768 " -0.079 2.00e-02 2.50e+03 pdb=" O PHE A 768 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA A 769 " 0.027 2.00e-02 2.50e+03 ... (remaining 1268 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 82 2.62 - 3.19: 6210 3.19 - 3.76: 10332 3.76 - 4.33: 14113 4.33 - 4.90: 23836 Nonbonded interactions: 54573 Sorted by model distance: nonbonded pdb=" OE1 GLU A 686 " pdb=" OG SER A 703 " model vdw 2.054 3.040 nonbonded pdb=" O LYS E 54 " pdb=" N SER E 111 " model vdw 2.251 3.120 nonbonded pdb=" O ILE A 610 " pdb=" OG1 THR A 614 " model vdw 2.299 3.040 nonbonded pdb=" O PRO A 695 " pdb=" OG1 THR A 707 " model vdw 2.302 3.040 nonbonded pdb=" O ALA A 528 " pdb=" NZ LYS A 783 " model vdw 2.311 3.120 ... (remaining 54568 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 Found NCS groups: ncs_group { reference = (chain 'E' and resid 35 through 133) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 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: 0.070 Process input model: 20.170 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 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 : 0.013 0.228 7408 Z= 0.814 Angle : 1.336 20.334 10050 Z= 0.977 Chirality : 0.050 0.325 1166 Planarity : 0.007 0.065 1271 Dihedral : 8.911 59.974 2669 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.80 % Allowed : 4.51 % Favored : 92.68 % 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: -1.42 (0.28), residues: 916 helix: 0.48 (0.34), residues: 214 sheet: -0.96 (0.38), residues: 207 loop : -1.59 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 812 HIS 0.003 0.000 HIS A 683 PHE 0.008 0.001 PHE A 696 TYR 0.018 0.001 TYR F 120 ARG 0.004 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.7726 (pt) cc_final: 0.7356 (pt) REVERT: A 116 GLN cc_start: 0.7932 (mt0) cc_final: 0.7700 (mt0) REVERT: A 212 LYS cc_start: 0.7471 (mttt) cc_final: 0.7267 (mtmt) REVERT: A 215 SER cc_start: 0.8933 (t) cc_final: 0.8372 (p) REVERT: A 219 HIS cc_start: 0.8182 (m170) cc_final: 0.7961 (m-70) REVERT: A 252 GLU cc_start: 0.7353 (tt0) cc_final: 0.6890 (mt-10) REVERT: A 269 ASP cc_start: 0.7550 (t0) cc_final: 0.7328 (t0) REVERT: A 275 ARG cc_start: 0.6981 (mtt180) cc_final: 0.6585 (mtt90) REVERT: A 369 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7324 (mt-10) REVERT: A 416 THR cc_start: 0.7240 (p) cc_final: 0.6849 (p) REVERT: A 437 ASN cc_start: 0.7195 (m-40) cc_final: 0.6917 (t0) REVERT: A 442 VAL cc_start: 0.7952 (OUTLIER) cc_final: 0.7577 (m) REVERT: A 690 SER cc_start: 0.8528 (p) cc_final: 0.8253 (m) REVERT: A 725 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.7629 (t80) REVERT: A 808 PHE cc_start: 0.6237 (m-80) cc_final: 0.5904 (m-80) REVERT: A 812 TRP cc_start: 0.6568 (OUTLIER) cc_final: 0.5671 (p90) outliers start: 23 outliers final: 6 residues processed: 204 average time/residue: 0.2407 time to fit residues: 63.9069 Evaluate side-chains 136 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 812 TRP Chi-restraints excluded: chain F residue 55 CYS Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 114 MET Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.0000 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 87 GLN A 218 GLN A 236 ASN A 311 GLN A 320 HIS A 354 ASN A 386 GLN A 417 ASN A 423 ASN A 556 ASN A 740 ASN A 756 ASN E 87 GLN E 127 HIS F 50 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.134776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.113501 restraints weight = 12652.871| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.86 r_work: 0.3324 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7408 Z= 0.229 Angle : 0.644 9.575 10050 Z= 0.326 Chirality : 0.045 0.179 1166 Planarity : 0.004 0.047 1271 Dihedral : 5.320 47.409 999 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.66 % Allowed : 9.76 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.28), residues: 916 helix: 1.86 (0.36), residues: 210 sheet: -1.04 (0.40), residues: 185 loop : -1.43 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 812 HIS 0.009 0.001 HIS E 50 PHE 0.021 0.001 PHE A 547 TYR 0.019 0.002 TYR A 801 ARG 0.004 0.000 ARG F 109 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 SER cc_start: 0.9282 (t) cc_final: 0.9029 (p) REVERT: A 539 TRP cc_start: 0.8153 (p-90) cc_final: 0.7909 (p-90) REVERT: A 690 SER cc_start: 0.8432 (p) cc_final: 0.8194 (m) REVERT: A 740 ASN cc_start: 0.5115 (OUTLIER) cc_final: 0.4883 (p0) REVERT: A 756 ASN cc_start: 0.7756 (m110) cc_final: 0.7278 (m-40) REVERT: A 808 PHE cc_start: 0.6342 (m-80) cc_final: 0.6095 (m-10) REVERT: E 73 SER cc_start: 0.8240 (p) cc_final: 0.8000 (m) REVERT: F 47 SER cc_start: 0.8260 (m) cc_final: 0.7647 (p) REVERT: F 109 ARG cc_start: 0.4586 (mtm180) cc_final: 0.4173 (mtm180) outliers start: 30 outliers final: 15 residues processed: 159 average time/residue: 0.1971 time to fit residues: 42.4569 Evaluate side-chains 128 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 127 HIS Chi-restraints excluded: chain F residue 55 CYS Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 71 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 116 GLN A 740 ASN A 797 ASN E 127 HIS F 42 HIS F 43 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.131993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.110174 restraints weight = 12745.512| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.92 r_work: 0.3277 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7408 Z= 0.246 Angle : 0.654 14.077 10050 Z= 0.331 Chirality : 0.045 0.264 1166 Planarity : 0.004 0.052 1271 Dihedral : 4.409 39.695 987 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.90 % Allowed : 13.05 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.28), residues: 916 helix: 1.91 (0.36), residues: 217 sheet: -1.27 (0.39), residues: 181 loop : -1.51 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 159 HIS 0.012 0.001 HIS E 127 PHE 0.019 0.001 PHE A 679 TYR 0.022 0.002 TYR A 725 ARG 0.007 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 215 SER cc_start: 0.9283 (t) cc_final: 0.9016 (p) REVERT: A 412 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7472 (pp) REVERT: A 690 SER cc_start: 0.8406 (p) cc_final: 0.8172 (m) REVERT: A 740 ASN cc_start: 0.5335 (OUTLIER) cc_final: 0.4807 (p0) REVERT: A 756 ASN cc_start: 0.7653 (OUTLIER) cc_final: 0.7306 (m-40) REVERT: A 757 CYS cc_start: 0.7802 (p) cc_final: 0.7524 (p) REVERT: A 812 TRP cc_start: 0.6305 (OUTLIER) cc_final: 0.5760 (p-90) REVERT: F 109 ARG cc_start: 0.4578 (mtm110) cc_final: 0.4072 (mtm180) outliers start: 32 outliers final: 13 residues processed: 140 average time/residue: 0.1789 time to fit residues: 34.4974 Evaluate side-chains 121 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 756 ASN Chi-restraints excluded: chain A residue 812 TRP Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 91 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 65 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 78 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 ASN A 437 ASN A 740 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.130714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.108907 restraints weight = 12751.158| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.85 r_work: 0.3261 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7408 Z= 0.269 Angle : 0.672 11.064 10050 Z= 0.339 Chirality : 0.045 0.228 1166 Planarity : 0.004 0.048 1271 Dihedral : 4.224 21.816 986 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 4.02 % Allowed : 13.29 % Favored : 82.68 % 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: -1.04 (0.28), residues: 916 helix: 1.84 (0.36), residues: 217 sheet: -1.32 (0.36), residues: 195 loop : -1.61 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 539 HIS 0.004 0.001 HIS A 256 PHE 0.020 0.001 PHE A 679 TYR 0.018 0.002 TYR A 725 ARG 0.008 0.001 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.831 Fit side-chains REVERT: A 215 SER cc_start: 0.9315 (t) cc_final: 0.9010 (p) REVERT: A 412 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7603 (pp) REVERT: A 690 SER cc_start: 0.8358 (p) cc_final: 0.8131 (m) REVERT: A 740 ASN cc_start: 0.5334 (OUTLIER) cc_final: 0.4774 (p0) REVERT: A 756 ASN cc_start: 0.7602 (OUTLIER) cc_final: 0.7269 (m-40) REVERT: A 812 TRP cc_start: 0.6258 (OUTLIER) cc_final: 0.5647 (p-90) REVERT: E 49 SER cc_start: 0.8807 (p) cc_final: 0.8561 (t) REVERT: F 40 MET cc_start: 0.7745 (ptm) cc_final: 0.7186 (ptt) REVERT: F 109 ARG cc_start: 0.4642 (mtm110) cc_final: 0.4169 (mtm180) outliers start: 33 outliers final: 16 residues processed: 132 average time/residue: 0.1849 time to fit residues: 33.4947 Evaluate side-chains 120 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 756 ASN Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 812 TRP Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 91 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 60 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 21 optimal weight: 0.0870 chunk 55 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.0570 chunk 11 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 740 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.133715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.112423 restraints weight = 12824.854| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.56 r_work: 0.3348 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 7408 Z= 0.153 Angle : 0.580 10.155 10050 Z= 0.292 Chirality : 0.042 0.193 1166 Planarity : 0.004 0.051 1271 Dihedral : 3.882 22.692 985 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.17 % Allowed : 14.27 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.28), residues: 916 helix: 2.12 (0.36), residues: 214 sheet: -1.29 (0.36), residues: 192 loop : -1.45 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 539 HIS 0.003 0.001 HIS A 219 PHE 0.018 0.001 PHE A 679 TYR 0.014 0.001 TYR A 725 ARG 0.008 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.787 Fit side-chains REVERT: A 147 ASP cc_start: 0.7833 (t70) cc_final: 0.7613 (p0) REVERT: A 215 SER cc_start: 0.9258 (t) cc_final: 0.8994 (p) REVERT: A 412 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7525 (pp) REVERT: A 539 TRP cc_start: 0.7894 (p-90) cc_final: 0.7615 (p-90) REVERT: A 690 SER cc_start: 0.8397 (p) cc_final: 0.8144 (m) REVERT: A 740 ASN cc_start: 0.5082 (OUTLIER) cc_final: 0.4521 (p0) REVERT: A 756 ASN cc_start: 0.7506 (OUTLIER) cc_final: 0.7171 (m-40) REVERT: A 812 TRP cc_start: 0.6002 (OUTLIER) cc_final: 0.5481 (p-90) REVERT: E 81 PHE cc_start: 0.6166 (m-10) cc_final: 0.5953 (m-10) REVERT: F 40 MET cc_start: 0.7588 (ptm) cc_final: 0.7202 (ptt) outliers start: 26 outliers final: 13 residues processed: 128 average time/residue: 0.2111 time to fit residues: 36.0778 Evaluate side-chains 116 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 756 ASN Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 812 TRP Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 127 HIS Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 91 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.8778 > 50: distance: 10 - 56: 3.996 distance: 26 - 139: 22.137 distance: 29 - 155: 17.989 distance: 85 - 120: 7.930 distance: 102 - 112: 11.170 distance: 112 - 113: 14.141 distance: 113 - 114: 24.052 distance: 113 - 116: 10.241 distance: 114 - 115: 18.516 distance: 114 - 120: 20.351 distance: 116 - 117: 23.822 distance: 116 - 118: 5.438 distance: 117 - 119: 8.297 distance: 120 - 121: 10.837 distance: 121 - 124: 11.543 distance: 122 - 123: 11.610 distance: 122 - 128: 9.671 distance: 124 - 125: 16.670 distance: 125 - 126: 5.608 distance: 125 - 127: 15.567 distance: 128 - 129: 9.807 distance: 129 - 130: 10.629 distance: 129 - 132: 13.992 distance: 130 - 131: 7.714 distance: 130 - 134: 3.584 distance: 132 - 133: 18.106 distance: 134 - 135: 7.341 distance: 135 - 136: 8.450 distance: 135 - 138: 7.751 distance: 136 - 137: 10.957 distance: 136 - 140: 4.825 distance: 138 - 139: 24.748 distance: 140 - 141: 12.782 distance: 141 - 142: 8.326 distance: 141 - 144: 17.768 distance: 142 - 143: 15.353 distance: 142 - 150: 5.370 distance: 144 - 145: 18.411 distance: 145 - 146: 12.411 distance: 145 - 147: 11.274 distance: 146 - 148: 16.456 distance: 147 - 149: 12.864 distance: 148 - 149: 8.209 distance: 150 - 151: 5.099 distance: 151 - 152: 6.058 distance: 151 - 154: 10.667 distance: 152 - 153: 8.863 distance: 152 - 156: 6.628 distance: 154 - 155: 14.132 distance: 156 - 157: 4.922 distance: 157 - 158: 8.869 distance: 157 - 160: 6.218 distance: 158 - 159: 3.373 distance: 158 - 165: 4.225 distance: 160 - 161: 12.325 distance: 161 - 162: 20.982 distance: 162 - 163: 15.389 distance: 162 - 164: 14.766 distance: 165 - 166: 3.975 distance: 166 - 167: 5.246 distance: 166 - 169: 4.382 distance: 167 - 168: 6.610 distance: 167 - 174: 12.766 distance: 169 - 170: 12.189 distance: 170 - 171: 9.998 distance: 171 - 172: 5.610 distance: 175 - 176: 10.020 distance: 175 - 178: 8.618 distance: 176 - 180: 5.546 distance: 179 - 206: 8.737 distance: 180 - 181: 6.280 distance: 181 - 182: 11.212 distance: 182 - 183: 3.933 distance: 184 - 185: 13.129 distance: 185 - 186: 11.093 distance: 185 - 187: 13.434