Starting phenix.real_space_refine on Sat Dec 28 01:17:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wvy_37876/12_2024/8wvy_37876.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wvy_37876/12_2024/8wvy_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_37876/12_2024/8wvy_37876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wvy_37876/12_2024/8wvy_37876.map" model { file = "/net/cci-nas-00/data/ceres_data/8wvy_37876/12_2024/8wvy_37876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wvy_37876/12_2024/8wvy_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-5532/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: 5.20, per 1000 atoms: 0.72 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: 1.51 Conformation dependent library (CDL) restraints added in 1.0 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: 0.75 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: 2.14 Time building geometry restraints manager: 1.84 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: 2.550 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.070 Find NCS groups from input model: 0.100 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.180 ------------------------------------------------------------------------------- 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 : 0.717 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: 0.2216 time to fit residues: 58.4746 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 : 1.021 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 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 : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.7692 (t0) cc_final: 0.7479 (t0) REVERT: A 116 GLN cc_start: 0.8140 (mt0) cc_final: 0.7736 (mt0) REVERT: A 212 LYS cc_start: 0.7582 (mttt) cc_final: 0.7340 (mtmt) REVERT: A 215 SER cc_start: 0.8991 (t) cc_final: 0.8405 (p) REVERT: A 219 HIS cc_start: 0.8299 (m170) cc_final: 0.7988 (m-70) REVERT: A 252 GLU cc_start: 0.7272 (tt0) cc_final: 0.6770 (mt-10) REVERT: A 269 ASP cc_start: 0.7630 (t0) cc_final: 0.7404 (t0) REVERT: A 275 ARG cc_start: 0.7201 (mtt180) cc_final: 0.6775 (mtt90) REVERT: A 369 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7459 (mt-10) REVERT: A 416 THR cc_start: 0.7416 (p) cc_final: 0.7025 (t) REVERT: A 437 ASN cc_start: 0.7198 (m-40) cc_final: 0.6907 (t0) REVERT: A 539 TRP cc_start: 0.7825 (p-90) cc_final: 0.7568 (p-90) REVERT: A 756 ASN cc_start: 0.7755 (m110) cc_final: 0.7307 (m-40) REVERT: A 808 PHE cc_start: 0.5862 (m-80) cc_final: 0.5619 (m-10) REVERT: E 46 ASP cc_start: 0.7678 (t0) cc_final: 0.7397 (t0) REVERT: E 73 SER cc_start: 0.7765 (p) cc_final: 0.7546 (m) REVERT: F 47 SER cc_start: 0.8190 (m) cc_final: 0.7495 (p) outliers start: 30 outliers final: 15 residues processed: 159 average time/residue: 0.1914 time to fit residues: 41.4246 Evaluate side-chains 133 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 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 46 optimal weight: 0.0020 chunk 25 optimal weight: 0.6980 chunk 69 optimal weight: 0.4980 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 797 ASN E 127 HIS F 42 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7408 Z= 0.184 Angle : 0.607 12.811 10050 Z= 0.307 Chirality : 0.043 0.254 1166 Planarity : 0.004 0.051 1271 Dihedral : 4.288 40.324 987 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.02 % Allowed : 12.20 % Favored : 83.78 % 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: -0.77 (0.28), residues: 916 helix: 2.12 (0.36), residues: 214 sheet: -1.28 (0.39), residues: 182 loop : -1.41 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 546 HIS 0.010 0.001 HIS E 127 PHE 0.019 0.001 PHE A 679 TYR 0.022 0.002 TYR A 725 ARG 0.003 0.000 ARG E 97 *********************** 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 157 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLN cc_start: 0.8137 (mt0) cc_final: 0.7730 (mt0) REVERT: A 212 LYS cc_start: 0.7544 (mttt) cc_final: 0.7305 (mtmt) REVERT: A 215 SER cc_start: 0.8973 (t) cc_final: 0.8410 (p) REVERT: A 219 HIS cc_start: 0.8286 (m170) cc_final: 0.8000 (m-70) REVERT: A 252 GLU cc_start: 0.7228 (tt0) cc_final: 0.6756 (mt-10) REVERT: A 269 ASP cc_start: 0.7653 (t0) cc_final: 0.7434 (t0) REVERT: A 275 ARG cc_start: 0.7215 (mtt180) cc_final: 0.6784 (mtt90) REVERT: A 369 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7446 (mt-10) REVERT: A 412 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6834 (pp) REVERT: A 416 THR cc_start: 0.7367 (p) cc_final: 0.7017 (t) REVERT: A 437 ASN cc_start: 0.7183 (m-40) cc_final: 0.6911 (t0) REVERT: A 539 TRP cc_start: 0.7762 (p-90) cc_final: 0.7555 (p-90) REVERT: A 756 ASN cc_start: 0.7627 (OUTLIER) cc_final: 0.7311 (m-40) REVERT: A 757 CYS cc_start: 0.7552 (p) cc_final: 0.7257 (p) REVERT: A 812 TRP cc_start: 0.5733 (OUTLIER) cc_final: 0.5251 (p-90) REVERT: F 114 MET cc_start: 0.5829 (tmm) cc_final: 0.5585 (tmm) outliers start: 33 outliers final: 17 residues processed: 150 average time/residue: 0.2093 time to fit residues: 43.0240 Evaluate side-chains 131 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 340 GLN Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 400 LEU 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 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 E residue 127 HIS Chi-restraints excluded: chain F residue 55 CYS 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 82 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 9 optimal weight: 0.0770 chunk 39 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 434 ASN E 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.3548 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= 0.235 Angle : 0.639 10.985 10050 Z= 0.321 Chirality : 0.044 0.221 1166 Planarity : 0.004 0.053 1271 Dihedral : 4.164 34.203 987 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.66 % Allowed : 12.20 % Favored : 84.15 % 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 (0.37), residues: 213 sheet: -1.24 (0.39), residues: 180 loop : -1.47 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 159 HIS 0.011 0.001 HIS E 127 PHE 0.013 0.001 PHE A 547 TYR 0.018 0.002 TYR A 725 ARG 0.003 0.000 ARG E 97 *********************** 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 140 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.811 Fit side-chains REVERT: A 116 GLN cc_start: 0.8154 (mt0) cc_final: 0.7718 (mt0) REVERT: A 212 LYS cc_start: 0.7556 (mttt) cc_final: 0.7239 (mtmm) REVERT: A 215 SER cc_start: 0.8950 (t) cc_final: 0.8396 (p) REVERT: A 219 HIS cc_start: 0.8293 (m170) cc_final: 0.8035 (m-70) REVERT: A 252 GLU cc_start: 0.7259 (tt0) cc_final: 0.6774 (mt-10) REVERT: A 275 ARG cc_start: 0.7267 (mtt180) cc_final: 0.6845 (mtt90) REVERT: A 369 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7442 (mt-10) REVERT: A 412 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6815 (pp) REVERT: A 416 THR cc_start: 0.7355 (p) cc_final: 0.6980 (t) REVERT: A 437 ASN cc_start: 0.7197 (m-40) cc_final: 0.6899 (t0) REVERT: A 756 ASN cc_start: 0.7620 (OUTLIER) cc_final: 0.7331 (m-40) REVERT: A 812 TRP cc_start: 0.5748 (OUTLIER) cc_final: 0.5176 (p-90) REVERT: E 49 SER cc_start: 0.8699 (p) cc_final: 0.8323 (t) outliers start: 30 outliers final: 16 residues processed: 134 average time/residue: 0.1847 time to fit residues: 34.1245 Evaluate side-chains 124 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 143 SER 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 756 ASN 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 50 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 61 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7408 Z= 0.235 Angle : 0.661 16.077 10050 Z= 0.326 Chirality : 0.044 0.213 1166 Planarity : 0.004 0.051 1271 Dihedral : 4.193 22.501 985 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.78 % Allowed : 13.17 % 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: -0.93 (0.28), residues: 916 helix: 2.05 (0.37), residues: 214 sheet: -1.36 (0.36), residues: 193 loop : -1.55 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 539 HIS 0.004 0.001 HIS A 256 PHE 0.022 0.001 PHE A 679 TYR 0.016 0.002 TYR A 725 ARG 0.003 0.000 ARG E 97 *********************** 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 139 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.869 Fit side-chains REVERT: A 87 GLN cc_start: 0.7716 (mt0) cc_final: 0.7384 (mt0) REVERT: A 116 GLN cc_start: 0.8117 (mt0) cc_final: 0.7677 (mt0) REVERT: A 212 LYS cc_start: 0.7534 (mttt) cc_final: 0.7223 (mtmm) REVERT: A 215 SER cc_start: 0.8979 (t) cc_final: 0.8343 (p) REVERT: A 219 HIS cc_start: 0.8289 (m170) cc_final: 0.8067 (m-70) REVERT: A 252 GLU cc_start: 0.7281 (tt0) cc_final: 0.6735 (mt-10) REVERT: A 275 ARG cc_start: 0.7292 (mtt180) cc_final: 0.6854 (mtt90) REVERT: A 344 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7451 (ttm) REVERT: A 412 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7061 (pp) REVERT: A 416 THR cc_start: 0.7288 (p) cc_final: 0.6919 (t) REVERT: A 437 ASN cc_start: 0.7230 (m-40) cc_final: 0.6945 (t0) REVERT: A 539 TRP cc_start: 0.7718 (p-90) cc_final: 0.7426 (p-90) REVERT: A 756 ASN cc_start: 0.7546 (m110) cc_final: 0.7241 (m-40) REVERT: A 812 TRP cc_start: 0.5593 (OUTLIER) cc_final: 0.5073 (p-90) REVERT: E 49 SER cc_start: 0.8691 (p) cc_final: 0.8324 (t) REVERT: E 81 PHE cc_start: 0.6340 (m-10) cc_final: 0.6094 (m-10) REVERT: F 40 MET cc_start: 0.7834 (ptm) cc_final: 0.7273 (ptt) outliers start: 31 outliers final: 18 residues processed: 134 average time/residue: 0.1881 time to fit residues: 34.2023 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 : 0.673 ------------------------------------------------------------------------------- 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 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 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 48 ILE 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 80 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 0.0870 chunk 73 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7408 Z= 0.224 Angle : 0.652 15.385 10050 Z= 0.321 Chirality : 0.044 0.202 1166 Planarity : 0.004 0.048 1271 Dihedral : 4.156 21.495 985 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.41 % Allowed : 13.66 % Favored : 82.93 % 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: -0.88 (0.28), residues: 916 helix: 2.12 (0.37), residues: 214 sheet: -1.38 (0.37), residues: 184 loop : -1.50 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 539 HIS 0.004 0.001 HIS A 256 PHE 0.019 0.001 PHE A 679 TYR 0.014 0.001 TYR A 725 ARG 0.002 0.000 ARG E 90 *********************** 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 136 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 87 GLN cc_start: 0.7661 (mt0) cc_final: 0.7329 (mt0) REVERT: A 116 GLN cc_start: 0.8109 (mt0) cc_final: 0.7678 (mt0) REVERT: A 212 LYS cc_start: 0.7531 (mttt) cc_final: 0.7219 (mtmm) REVERT: A 215 SER cc_start: 0.8984 (t) cc_final: 0.8349 (p) REVERT: A 219 HIS cc_start: 0.8290 (m170) cc_final: 0.8074 (m-70) REVERT: A 252 GLU cc_start: 0.7285 (tt0) cc_final: 0.6740 (mt-10) REVERT: A 275 ARG cc_start: 0.7310 (mtt180) cc_final: 0.6868 (mtt90) REVERT: A 344 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7412 (ttm) REVERT: A 412 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7132 (pp) REVERT: A 416 THR cc_start: 0.7300 (p) cc_final: 0.6916 (t) REVERT: A 437 ASN cc_start: 0.7191 (m-40) cc_final: 0.6779 (t0) REVERT: A 539 TRP cc_start: 0.7756 (p-90) cc_final: 0.7446 (p-90) REVERT: A 756 ASN cc_start: 0.7572 (OUTLIER) cc_final: 0.7243 (m-40) REVERT: A 812 TRP cc_start: 0.5628 (OUTLIER) cc_final: 0.5095 (p-90) REVERT: E 46 ASP cc_start: 0.7794 (t0) cc_final: 0.7539 (t0) REVERT: E 49 SER cc_start: 0.8685 (p) cc_final: 0.8325 (t) REVERT: E 81 PHE cc_start: 0.6403 (m-10) cc_final: 0.6199 (m-10) REVERT: E 107 ARG cc_start: 0.8503 (mmm-85) cc_final: 0.8286 (ttm-80) REVERT: F 40 MET cc_start: 0.7899 (ptm) cc_final: 0.7345 (ptt) outliers start: 28 outliers final: 19 residues processed: 131 average time/residue: 0.2192 time to fit residues: 38.0976 Evaluate side-chains 132 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 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 610 ILE Chi-restraints excluded: chain A residue 620 VAL 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 E residue 127 HIS Chi-restraints excluded: chain F residue 48 ILE 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: 0.1980 chunk 50 optimal weight: 0.3980 chunk 65 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 88 optimal weight: 0.0170 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 7408 Z= 0.157 Angle : 0.589 12.937 10050 Z= 0.291 Chirality : 0.042 0.174 1166 Planarity : 0.004 0.047 1271 Dihedral : 3.876 21.638 985 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.68 % Allowed : 15.00 % 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: -0.84 (0.28), residues: 916 helix: 2.12 (0.37), residues: 215 sheet: -1.40 (0.38), residues: 176 loop : -1.45 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 539 HIS 0.003 0.001 HIS A 299 PHE 0.010 0.001 PHE A 547 TYR 0.014 0.001 TYR A 725 ARG 0.003 0.000 ARG E 90 *********************** 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: 22 poor density : 106 time to evaluate : 0.793 Fit side-chains REVERT: A 87 GLN cc_start: 0.7625 (mt0) cc_final: 0.7286 (mt0) REVERT: A 116 GLN cc_start: 0.8091 (mt0) cc_final: 0.7669 (mt0) REVERT: A 212 LYS cc_start: 0.7477 (mttt) cc_final: 0.7229 (mtmt) REVERT: A 215 SER cc_start: 0.8990 (t) cc_final: 0.8375 (p) REVERT: A 219 HIS cc_start: 0.8269 (m170) cc_final: 0.8066 (m-70) REVERT: A 242 GLN cc_start: 0.7721 (tt0) cc_final: 0.7363 (tm-30) REVERT: A 252 GLU cc_start: 0.7226 (tt0) cc_final: 0.6732 (mt-10) REVERT: A 275 ARG cc_start: 0.7297 (mtt180) cc_final: 0.6843 (mtt90) REVERT: A 412 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6864 (pp) REVERT: A 416 THR cc_start: 0.7315 (p) cc_final: 0.6944 (t) REVERT: A 437 ASN cc_start: 0.7160 (m-40) cc_final: 0.6744 (t0) REVERT: A 539 TRP cc_start: 0.7688 (p-90) cc_final: 0.7364 (p-90) REVERT: A 756 ASN cc_start: 0.7386 (m110) cc_final: 0.7047 (m-40) REVERT: E 49 SER cc_start: 0.8662 (p) cc_final: 0.8319 (t) REVERT: E 107 ARG cc_start: 0.8491 (mmm-85) cc_final: 0.8269 (ttm-80) REVERT: F 40 MET cc_start: 0.7880 (ptm) cc_final: 0.7345 (ptt) outliers start: 22 outliers final: 13 residues processed: 124 average time/residue: 0.2217 time to fit residues: 36.3209 Evaluate side-chains 115 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 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 757 CYS 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 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 26 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7408 Z= 0.291 Angle : 0.700 13.317 10050 Z= 0.348 Chirality : 0.046 0.220 1166 Planarity : 0.004 0.048 1271 Dihedral : 4.340 25.012 985 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.80 % Allowed : 15.37 % Favored : 81.83 % 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: 1.87 (0.36), residues: 215 sheet: -1.34 (0.39), residues: 170 loop : -1.63 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 812 HIS 0.005 0.001 HIS A 209 PHE 0.010 0.001 PHE A 197 TYR 0.020 0.002 TYR A 801 ARG 0.003 0.000 ARG F 41 *********************** 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 131 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 87 GLN cc_start: 0.7723 (mt0) cc_final: 0.7338 (mt0) REVERT: A 116 GLN cc_start: 0.8091 (mt0) cc_final: 0.7657 (mt0) REVERT: A 150 GLU cc_start: 0.7872 (tt0) cc_final: 0.7572 (tt0) REVERT: A 212 LYS cc_start: 0.7540 (mttt) cc_final: 0.7237 (mtmm) REVERT: A 215 SER cc_start: 0.8970 (t) cc_final: 0.8326 (p) REVERT: A 252 GLU cc_start: 0.7339 (tt0) cc_final: 0.6807 (mt-10) REVERT: A 275 ARG cc_start: 0.7355 (mtt180) cc_final: 0.6854 (mtt90) REVERT: A 344 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7452 (ttm) REVERT: A 412 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.6998 (pp) REVERT: A 416 THR cc_start: 0.7291 (p) cc_final: 0.6859 (t) REVERT: A 437 ASN cc_start: 0.7224 (m-40) cc_final: 0.6773 (t0) REVERT: A 539 TRP cc_start: 0.7830 (p-90) cc_final: 0.7506 (p-90) REVERT: A 756 ASN cc_start: 0.7532 (m110) cc_final: 0.7160 (m-40) REVERT: E 46 ASP cc_start: 0.7811 (t0) cc_final: 0.7530 (t0) REVERT: E 107 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.8268 (ttm-80) REVERT: F 40 MET cc_start: 0.7883 (ptm) cc_final: 0.7362 (ptt) outliers start: 23 outliers final: 18 residues processed: 126 average time/residue: 0.2066 time to fit residues: 34.6088 Evaluate side-chains 126 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 344 MET 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 757 CYS Chi-restraints excluded: chain A residue 761 CYS 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 E residue 127 HIS Chi-restraints excluded: chain F residue 48 ILE 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 84 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 0.0170 chunk 54 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7408 Z= 0.238 Angle : 0.650 12.561 10050 Z= 0.323 Chirality : 0.044 0.182 1166 Planarity : 0.004 0.048 1271 Dihedral : 4.181 22.480 985 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.80 % Allowed : 16.34 % Favored : 80.85 % 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: -1.01 (0.28), residues: 916 helix: 2.14 (0.36), residues: 209 sheet: -1.41 (0.39), residues: 167 loop : -1.65 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 812 HIS 0.004 0.001 HIS A 256 PHE 0.011 0.001 PHE A 547 TYR 0.017 0.002 TYR A 801 ARG 0.004 0.000 ARG F 97 *********************** 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 131 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.780 Fit side-chains REVERT: A 87 GLN cc_start: 0.7686 (mt0) cc_final: 0.7299 (mt0) REVERT: A 116 GLN cc_start: 0.8140 (mt0) cc_final: 0.7568 (mt0) REVERT: A 150 GLU cc_start: 0.7883 (tt0) cc_final: 0.7597 (tt0) REVERT: A 212 LYS cc_start: 0.7516 (mttt) cc_final: 0.7209 (mtmm) REVERT: A 252 GLU cc_start: 0.7290 (tt0) cc_final: 0.6745 (mt-10) REVERT: A 275 ARG cc_start: 0.7336 (mtt180) cc_final: 0.6843 (mtt90) REVERT: A 412 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7369 (pp) REVERT: A 416 THR cc_start: 0.7296 (p) cc_final: 0.6858 (t) REVERT: A 437 ASN cc_start: 0.7218 (m-40) cc_final: 0.6762 (t0) REVERT: A 539 TRP cc_start: 0.7751 (p-90) cc_final: 0.7440 (p-90) REVERT: A 756 ASN cc_start: 0.7511 (OUTLIER) cc_final: 0.7147 (m-40) REVERT: E 46 ASP cc_start: 0.7784 (t0) cc_final: 0.7508 (t0) REVERT: E 107 ARG cc_start: 0.8508 (mmm-85) cc_final: 0.8275 (ttm-80) REVERT: F 40 MET cc_start: 0.7925 (ptm) cc_final: 0.7410 (ptt) outliers start: 23 outliers final: 18 residues processed: 126 average time/residue: 0.2066 time to fit residues: 34.8460 Evaluate side-chains 126 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 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 756 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 48 ILE 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 41 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 57 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7408 Z= 0.332 Angle : 0.725 12.804 10050 Z= 0.359 Chirality : 0.047 0.182 1166 Planarity : 0.005 0.049 1271 Dihedral : 4.514 22.242 985 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.68 % Allowed : 16.22 % Favored : 81.10 % 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: -1.10 (0.28), residues: 916 helix: 2.02 (0.36), residues: 208 sheet: -1.49 (0.39), residues: 174 loop : -1.66 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 812 HIS 0.006 0.001 HIS A 209 PHE 0.016 0.001 PHE A 808 TYR 0.014 0.002 TYR A 725 ARG 0.007 0.001 ARG F 97 ********************** 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 126 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.867 Fit side-chains REVERT: A 87 GLN cc_start: 0.7770 (mt0) cc_final: 0.7360 (mt0) REVERT: A 116 GLN cc_start: 0.8107 (mt0) cc_final: 0.7536 (mt0) REVERT: A 150 GLU cc_start: 0.7881 (tt0) cc_final: 0.7652 (tt0) REVERT: A 212 LYS cc_start: 0.7538 (mttt) cc_final: 0.7232 (mtmm) REVERT: A 242 GLN cc_start: 0.7711 (tt0) cc_final: 0.7269 (tm-30) REVERT: A 252 GLU cc_start: 0.7370 (tt0) cc_final: 0.6799 (mt-10) REVERT: A 275 ARG cc_start: 0.7342 (mtt180) cc_final: 0.6858 (mtt90) REVERT: A 344 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7511 (ttm) REVERT: A 412 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7296 (pp) REVERT: A 416 THR cc_start: 0.7249 (p) cc_final: 0.6801 (t) REVERT: A 437 ASN cc_start: 0.7261 (m-40) cc_final: 0.6788 (t0) REVERT: A 539 TRP cc_start: 0.7735 (p-90) cc_final: 0.7447 (p-90) REVERT: A 756 ASN cc_start: 0.7580 (OUTLIER) cc_final: 0.7167 (m-40) REVERT: E 46 ASP cc_start: 0.7815 (t0) cc_final: 0.7538 (t0) REVERT: E 107 ARG cc_start: 0.8505 (mmm-85) cc_final: 0.8269 (ttm-80) REVERT: F 40 MET cc_start: 0.7895 (ptm) cc_final: 0.7401 (ptt) outliers start: 22 outliers final: 19 residues processed: 118 average time/residue: 0.2126 time to fit residues: 33.3311 Evaluate side-chains 126 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 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 610 ILE Chi-restraints excluded: chain A residue 620 VAL 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 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 48 ILE 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 67 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.129560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.108677 restraints weight = 12679.043| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.44 r_work: 0.3287 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7408 Z= 0.236 Angle : 0.657 12.233 10050 Z= 0.326 Chirality : 0.045 0.162 1166 Planarity : 0.004 0.048 1271 Dihedral : 4.283 20.531 985 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.93 % Allowed : 15.98 % Favored : 81.10 % 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: -1.08 (0.28), residues: 916 helix: 2.14 (0.37), residues: 209 sheet: -1.51 (0.38), residues: 173 loop : -1.70 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 812 HIS 0.004 0.001 HIS A 256 PHE 0.011 0.001 PHE A 547 TYR 0.016 0.002 TYR A 801 ARG 0.007 0.000 ARG F 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2092.21 seconds wall clock time: 41 minutes 16.72 seconds (2476.72 seconds total)