Starting phenix.real_space_refine on Sun May 11 01:34:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wvy_37876/05_2025/8wvy_37876.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wvy_37876/05_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_37876/05_2025/8wvy_37876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wvy_37876/05_2025/8wvy_37876.map" model { file = "/net/cci-nas-00/data/ceres_data/8wvy_37876/05_2025/8wvy_37876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wvy_37876/05_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-5687/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: 5.49, per 1000 atoms: 0.76 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: 1.79 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.88 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: 2.22 Time building geometry restraints manager: 2.08 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: 3.320 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: 0.050 Set scattering table: 0.070 Process input model: 21.380 Find NCS groups from input model: 0.130 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.260 ------------------------------------------------------------------------------- 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 : 0.015 0.448 7425 Z= 1.028 Angle : 1.372 21.006 10084 Z= 0.987 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 Details of bonding type rmsd hydrogen bonds : bond 0.26756 ( 223) hydrogen bonds : angle 7.14129 ( 651) SS BOND : bond 0.18129 ( 17) SS BOND : angle 5.50278 ( 34) covalent geometry : bond 0.01253 ( 7408) covalent geometry : angle 1.33618 (10050) *********************** 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 : 0.746 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: 0.2062 time to fit residues: 54.2604 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 : 0.739 ------------------------------------------------------------------------------- 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: 2.9990 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 7425 Z= 0.149 Angle : 0.652 9.575 10084 Z= 0.329 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 Details of bonding type rmsd hydrogen bonds : bond 0.06171 ( 223) hydrogen bonds : angle 4.83505 ( 651) SS BOND : bond 0.00429 ( 17) SS BOND : angle 1.80766 ( 34) covalent geometry : bond 0.00345 ( 7408) covalent geometry : angle 0.64442 (10050) *********************** 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 : 0.701 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: 0.1883 time to fit residues: 40.4458 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 : 0.834 ------------------------------------------------------------------------------- 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 7425 Z= 0.158 Angle : 0.671 14.077 10084 Z= 0.338 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 Details of bonding type rmsd hydrogen bonds : bond 0.05778 ( 223) hydrogen bonds : angle 4.56110 ( 651) SS BOND : bond 0.00458 ( 17) SS BOND : angle 2.68224 ( 34) covalent geometry : bond 0.00371 ( 7408) covalent geometry : angle 0.65401 (10050) *********************** 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 : 0.841 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: 0.1831 time to fit residues: 34.9855 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 : 0.785 ------------------------------------------------------------------------------- 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 7425 Z= 0.167 Angle : 0.689 11.064 10084 Z= 0.347 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 Details of bonding type rmsd hydrogen bonds : bond 0.05502 ( 223) hydrogen bonds : angle 4.58840 ( 651) SS BOND : bond 0.00744 ( 17) SS BOND : angle 2.75785 ( 34) covalent geometry : bond 0.00406 ( 7408) covalent geometry : angle 0.67173 (10050) *********************** 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 : 0.826 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: 0.1788 time to fit residues: 32.3276 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 : 0.804 ------------------------------------------------------------------------------- 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: 2.9990 chunk 80 optimal weight: 4.9990 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: 0.0030 chunk 11 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.3568 ------------------------------------------------------------------------------- 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 = 0.3909 r_free = 0.3909 target = 0.133176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.111883 restraints weight = 12810.255| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.56 r_work: 0.3337 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 7425 Z= 0.111 Angle : 0.604 10.226 10084 Z= 0.304 Chirality : 0.042 0.200 1166 Planarity : 0.004 0.051 1271 Dihedral : 3.942 22.341 985 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.54 % Allowed : 13.90 % 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: -0.84 (0.28), residues: 916 helix: 2.10 (0.36), residues: 214 sheet: -1.32 (0.36), residues: 192 loop : -1.47 (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 Details of bonding type rmsd hydrogen bonds : bond 0.04321 ( 223) hydrogen bonds : angle 4.36048 ( 651) SS BOND : bond 0.00445 ( 17) SS BOND : angle 2.30208 ( 34) covalent geometry : bond 0.00248 ( 7408) covalent geometry : angle 0.59051 (10050) *********************** 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 133 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.775 Fit side-chains REVERT: A 215 SER cc_start: 0.9264 (t) cc_final: 0.8992 (p) REVERT: A 412 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7535 (pp) REVERT: A 539 TRP cc_start: 0.7950 (p-90) cc_final: 0.7690 (p-90) REVERT: A 690 SER cc_start: 0.8395 (p) cc_final: 0.8144 (m) REVERT: A 740 ASN cc_start: 0.5003 (OUTLIER) cc_final: 0.4433 (p0) REVERT: A 756 ASN cc_start: 0.7547 (OUTLIER) cc_final: 0.7208 (m-40) REVERT: A 812 TRP cc_start: 0.6024 (OUTLIER) cc_final: 0.5500 (p-90) REVERT: E 81 PHE cc_start: 0.6189 (m-10) cc_final: 0.5970 (m-10) REVERT: F 40 MET cc_start: 0.7673 (ptm) cc_final: 0.7273 (ptt) outliers start: 29 outliers final: 17 residues processed: 128 average time/residue: 0.1964 time to fit residues: 34.1152 Evaluate side-chains 120 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 217 SER 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 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 761 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 ************** Weight determination summary: number of chunks: 92 random chunks: chunk 55 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 21 optimal weight: 0.0770 chunk 70 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.132275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.110741 restraints weight = 12949.455| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.73 r_work: 0.3309 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7425 Z= 0.122 Angle : 0.622 9.693 10084 Z= 0.311 Chirality : 0.043 0.181 1166 Planarity : 0.004 0.049 1271 Dihedral : 3.946 22.450 985 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.29 % Allowed : 14.39 % Favored : 82.32 % 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: 2.09 (0.36), residues: 215 sheet: -1.26 (0.38), residues: 176 loop : -1.49 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 539 HIS 0.003 0.001 HIS A 256 PHE 0.023 0.001 PHE A 679 TYR 0.014 0.001 TYR A 725 ARG 0.003 0.000 ARG E 97 Details of bonding type rmsd hydrogen bonds : bond 0.04451 ( 223) hydrogen bonds : angle 4.33481 ( 651) SS BOND : bond 0.00510 ( 17) SS BOND : angle 2.40477 ( 34) covalent geometry : bond 0.00285 ( 7408) covalent geometry : angle 0.60709 (10050) *********************** REFINEMENT MACRO_CYCLE 6 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: 27 poor density : 105 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 215 SER cc_start: 0.9279 (t) cc_final: 0.9022 (p) REVERT: A 412 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7667 (pp) REVERT: A 539 TRP cc_start: 0.7957 (p-90) cc_final: 0.7690 (p-90) REVERT: A 690 SER cc_start: 0.8381 (p) cc_final: 0.8124 (m) REVERT: A 740 ASN cc_start: 0.5041 (OUTLIER) cc_final: 0.4410 (p0) REVERT: A 756 ASN cc_start: 0.7462 (m110) cc_final: 0.7147 (m-40) REVERT: F 40 MET cc_start: 0.7620 (ptm) cc_final: 0.7239 (ptt) REVERT: F 129 GLU cc_start: 0.8500 (pt0) cc_final: 0.8290 (pt0) outliers start: 27 outliers final: 19 residues processed: 129 average time/residue: 0.1893 time to fit residues: 32.9823 Evaluate side-chains 123 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 217 SER 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 757 CYS Chi-restraints excluded: chain A residue 761 CYS 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 119 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.0570 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.130630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.109689 restraints weight = 12788.249| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.58 r_work: 0.3269 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7425 Z= 0.152 Angle : 0.654 9.270 10084 Z= 0.328 Chirality : 0.044 0.196 1166 Planarity : 0.004 0.049 1271 Dihedral : 4.131 20.347 985 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.29 % Allowed : 14.76 % Favored : 81.95 % 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: -0.97 (0.28), residues: 916 helix: 1.96 (0.37), residues: 214 sheet: -1.35 (0.38), residues: 180 loop : -1.56 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 812 HIS 0.004 0.001 HIS A 256 PHE 0.020 0.001 PHE A 679 TYR 0.025 0.002 TYR A 801 ARG 0.004 0.000 ARG E 97 Details of bonding type rmsd hydrogen bonds : bond 0.04981 ( 223) hydrogen bonds : angle 4.43169 ( 651) SS BOND : bond 0.00505 ( 17) SS BOND : angle 2.43562 ( 34) covalent geometry : bond 0.00366 ( 7408) covalent geometry : angle 0.63911 (10050) *********************** REFINEMENT MACRO_CYCLE 7 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 128 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 215 SER cc_start: 0.9283 (t) cc_final: 0.9017 (p) REVERT: A 412 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7625 (pp) REVERT: A 539 TRP cc_start: 0.8007 (p-90) cc_final: 0.7745 (p-90) REVERT: A 690 SER cc_start: 0.8321 (p) cc_final: 0.8077 (m) REVERT: A 740 ASN cc_start: 0.4761 (OUTLIER) cc_final: 0.3807 (p0) REVERT: A 756 ASN cc_start: 0.7487 (m110) cc_final: 0.7157 (m-40) REVERT: A 814 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8703 (mt) REVERT: E 107 ARG cc_start: 0.8327 (ttm-80) cc_final: 0.8036 (ttm-80) REVERT: F 40 MET cc_start: 0.7674 (ptm) cc_final: 0.7292 (ptt) REVERT: F 129 GLU cc_start: 0.8508 (pt0) cc_final: 0.8295 (pt0) outliers start: 27 outliers final: 19 residues processed: 124 average time/residue: 0.2440 time to fit residues: 40.9064 Evaluate side-chains 121 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 307 SER 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 757 CYS Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 814 LEU 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 119 THR Chi-restraints excluded: chain E residue 127 HIS Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 126 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 86 optimal weight: 4.9990 chunk 16 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.129373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.108336 restraints weight = 12828.917| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.68 r_work: 0.3251 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7425 Z= 0.172 Angle : 0.700 13.177 10084 Z= 0.351 Chirality : 0.045 0.207 1166 Planarity : 0.004 0.050 1271 Dihedral : 4.306 25.960 985 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.05 % Allowed : 15.73 % Favored : 81.22 % 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: -1.07 (0.28), residues: 916 helix: 1.81 (0.36), residues: 214 sheet: -1.26 (0.39), residues: 170 loop : -1.66 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 812 HIS 0.005 0.001 HIS A 256 PHE 0.018 0.001 PHE A 679 TYR 0.012 0.002 TYR A 801 ARG 0.003 0.000 ARG E 97 Details of bonding type rmsd hydrogen bonds : bond 0.05233 ( 223) hydrogen bonds : angle 4.47484 ( 651) SS BOND : bond 0.00506 ( 17) SS BOND : angle 2.95018 ( 34) covalent geometry : bond 0.00421 ( 7408) covalent geometry : angle 0.67938 (10050) *********************** REFINEMENT MACRO_CYCLE 8 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 129 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 215 SER cc_start: 0.9288 (t) cc_final: 0.8999 (p) REVERT: A 242 GLN cc_start: 0.8127 (tt0) cc_final: 0.7874 (tm-30) REVERT: A 412 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7664 (pp) REVERT: A 539 TRP cc_start: 0.8034 (p-90) cc_final: 0.7774 (p-90) REVERT: A 690 SER cc_start: 0.8331 (p) cc_final: 0.8082 (m) REVERT: A 740 ASN cc_start: 0.4476 (OUTLIER) cc_final: 0.3585 (p0) REVERT: A 756 ASN cc_start: 0.7544 (m110) cc_final: 0.7166 (m-40) REVERT: F 40 MET cc_start: 0.7701 (ptm) cc_final: 0.7318 (ptt) REVERT: F 129 GLU cc_start: 0.8498 (pt0) cc_final: 0.8287 (pt0) outliers start: 25 outliers final: 20 residues processed: 126 average time/residue: 0.2082 time to fit residues: 35.5098 Evaluate side-chains 122 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 589 ILE 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 757 CYS Chi-restraints excluded: chain A residue 761 CYS 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 119 THR Chi-restraints excluded: chain E residue 127 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 126 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 90 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 88 optimal weight: 0.0040 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.129903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.108717 restraints weight = 12841.929| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.52 r_work: 0.3279 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7425 Z= 0.154 Angle : 0.683 11.801 10084 Z= 0.342 Chirality : 0.045 0.175 1166 Planarity : 0.004 0.050 1271 Dihedral : 4.257 23.328 985 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.93 % Allowed : 16.83 % 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: -1.09 (0.28), residues: 916 helix: 1.86 (0.37), residues: 214 sheet: -1.37 (0.39), residues: 176 loop : -1.66 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 812 HIS 0.004 0.001 HIS A 256 PHE 0.017 0.001 PHE A 679 TYR 0.013 0.001 TYR A 801 ARG 0.004 0.000 ARG E 97 Details of bonding type rmsd hydrogen bonds : bond 0.04926 ( 223) hydrogen bonds : angle 4.41369 ( 651) SS BOND : bond 0.00566 ( 17) SS BOND : angle 3.20429 ( 34) covalent geometry : bond 0.00375 ( 7408) covalent geometry : angle 0.65846 (10050) *********************** REFINEMENT MACRO_CYCLE 9 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 125 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 215 SER cc_start: 0.9287 (t) cc_final: 0.8992 (p) REVERT: A 242 GLN cc_start: 0.8095 (tt0) cc_final: 0.7850 (tm-30) REVERT: A 412 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7695 (pp) REVERT: A 539 TRP cc_start: 0.7980 (p-90) cc_final: 0.7714 (p-90) REVERT: A 690 SER cc_start: 0.8284 (p) cc_final: 0.8025 (m) REVERT: A 740 ASN cc_start: 0.4328 (OUTLIER) cc_final: 0.3525 (p0) REVERT: F 40 MET cc_start: 0.7638 (ptm) cc_final: 0.7260 (ptt) REVERT: F 129 GLU cc_start: 0.8447 (pt0) cc_final: 0.8228 (pt0) outliers start: 24 outliers final: 18 residues processed: 122 average time/residue: 0.1895 time to fit residues: 30.9501 Evaluate side-chains 121 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 307 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 589 ILE 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 757 CYS Chi-restraints excluded: chain A residue 761 CYS 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 119 THR Chi-restraints excluded: chain E residue 127 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 126 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 32 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.127387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.106327 restraints weight = 13012.898| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.66 r_work: 0.3224 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7425 Z= 0.229 Angle : 0.779 12.040 10084 Z= 0.387 Chirality : 0.048 0.178 1166 Planarity : 0.005 0.051 1271 Dihedral : 4.643 23.223 985 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.93 % Allowed : 16.83 % 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: -1.32 (0.27), residues: 916 helix: 1.63 (0.36), residues: 215 sheet: -1.51 (0.38), residues: 175 loop : -1.80 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 812 HIS 0.007 0.001 HIS A 209 PHE 0.016 0.002 PHE A 679 TYR 0.011 0.002 TYR A 725 ARG 0.005 0.001 ARG F 97 Details of bonding type rmsd hydrogen bonds : bond 0.05896 ( 223) hydrogen bonds : angle 4.53114 ( 651) SS BOND : bond 0.00556 ( 17) SS BOND : angle 3.37007 ( 34) covalent geometry : bond 0.00572 ( 7408) covalent geometry : angle 0.75507 (10050) ********************** REFINEMENT MACRO_CYCLE 10 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 123 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.841 Fit side-chains REVERT: A 242 GLN cc_start: 0.8126 (tt0) cc_final: 0.7853 (tm-30) REVERT: A 412 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8131 (pp) REVERT: A 539 TRP cc_start: 0.7952 (p-90) cc_final: 0.7710 (p-90) REVERT: A 690 SER cc_start: 0.8299 (p) cc_final: 0.7997 (m) REVERT: A 740 ASN cc_start: 0.4138 (OUTLIER) cc_final: 0.3239 (p0) REVERT: F 109 ARG cc_start: 0.4788 (mtm110) cc_final: 0.4308 (mtm110) REVERT: F 129 GLU cc_start: 0.8543 (pt0) cc_final: 0.8326 (pt0) outliers start: 24 outliers final: 21 residues processed: 119 average time/residue: 0.1971 time to fit residues: 31.4559 Evaluate side-chains 121 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 589 ILE 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 757 CYS Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain E residue 39 CYS 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 109 ARG Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 127 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 126 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.129327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.108263 restraints weight = 12847.304| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.50 r_work: 0.3278 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7425 Z= 0.148 Angle : 0.674 10.774 10084 Z= 0.336 Chirality : 0.044 0.161 1166 Planarity : 0.004 0.051 1271 Dihedral : 4.334 21.633 985 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.32 % Allowed : 17.07 % Favored : 80.61 % 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: -1.21 (0.28), residues: 916 helix: 1.71 (0.37), residues: 218 sheet: -1.40 (0.38), residues: 175 loop : -1.76 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 812 HIS 0.004 0.001 HIS A 256 PHE 0.016 0.001 PHE A 679 TYR 0.013 0.001 TYR A 801 ARG 0.006 0.000 ARG F 97 Details of bonding type rmsd hydrogen bonds : bond 0.04906 ( 223) hydrogen bonds : angle 4.27152 ( 651) SS BOND : bond 0.00423 ( 17) SS BOND : angle 2.74291 ( 34) covalent geometry : bond 0.00356 ( 7408) covalent geometry : angle 0.65592 (10050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4427.45 seconds wall clock time: 78 minutes 31.45 seconds (4711.45 seconds total)