Starting phenix.real_space_refine on Wed Mar 12 04:17:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wvy_37876/03_2025/8wvy_37876.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wvy_37876/03_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_37876/03_2025/8wvy_37876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wvy_37876/03_2025/8wvy_37876.map" model { file = "/net/cci-nas-00/data/ceres_data/8wvy_37876/03_2025/8wvy_37876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wvy_37876/03_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-5624/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: 5.44, per 1000 atoms: 0.75 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: 1.70 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: 0.92 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: 2.08 Time building geometry restraints manager: 2.04 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: 2.870 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: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.950 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.350 ------------------------------------------------------------------------------- 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 : 0.785 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: 0.2160 time to fit residues: 56.7702 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 : 0.789 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.9980 chunk 83 optimal weight: 0.9980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 87 GLN A 218 GLN A 236 ASN A 311 GLN A 320 HIS A 354 ASN A 386 GLN A 417 ASN A 423 ASN A 556 ASN A 740 ASN A 756 ASN E 87 GLN E 127 HIS F 50 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.134776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.113501 restraints weight = 12652.868| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.86 r_work: 0.3324 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7408 Z= 0.229 Angle : 0.644 9.575 10050 Z= 0.326 Chirality : 0.045 0.179 1166 Planarity : 0.004 0.047 1271 Dihedral : 5.320 47.409 999 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.66 % Allowed : 9.76 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.28), residues: 916 helix: 1.86 (0.36), residues: 210 sheet: -1.04 (0.40), residues: 185 loop : -1.43 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 812 HIS 0.009 0.001 HIS E 50 PHE 0.021 0.001 PHE A 547 TYR 0.019 0.002 TYR A 801 ARG 0.004 0.000 ARG F 109 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.780 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: 0.7908 (p-90) REVERT: A 690 SER cc_start: 0.8433 (p) cc_final: 0.8195 (m) REVERT: A 740 ASN cc_start: 0.5124 (OUTLIER) cc_final: 0.4890 (p0) REVERT: A 756 ASN cc_start: 0.7755 (m110) cc_final: 0.7274 (m-40) REVERT: A 808 PHE cc_start: 0.6346 (m-80) cc_final: 0.6098 (m-10) REVERT: E 73 SER cc_start: 0.8240 (p) cc_final: 0.7999 (m) REVERT: F 47 SER cc_start: 0.8260 (m) cc_final: 0.7647 (p) REVERT: F 109 ARG cc_start: 0.4585 (mtm180) cc_final: 0.4172 (mtm180) outliers start: 30 outliers final: 15 residues processed: 159 average time/residue: 0.1908 time to fit residues: 41.1391 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 : 0.873 ------------------------------------------------------------------------------- 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: 0.3980 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3901 r_free = 0.3901 target = 0.132275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.110426 restraints weight = 12751.527| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.93 r_work: 0.3279 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7408 Z= 0.233 Angle : 0.645 13.307 10050 Z= 0.326 Chirality : 0.045 0.273 1166 Planarity : 0.004 0.051 1271 Dihedral : 4.387 39.765 987 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.90 % Allowed : 12.68 % Favored : 83.41 % 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: 2.00 (0.36), residues: 214 sheet: -1.26 (0.39), residues: 181 loop : -1.50 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 159 HIS 0.014 0.001 HIS E 127 PHE 0.018 0.001 PHE A 679 TYR 0.023 0.002 TYR A 725 ARG 0.007 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 215 SER cc_start: 0.9284 (t) cc_final: 0.9020 (p) REVERT: A 412 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7465 (pp) REVERT: A 690 SER cc_start: 0.8435 (p) cc_final: 0.8203 (m) REVERT: A 740 ASN cc_start: 0.5323 (OUTLIER) cc_final: 0.4808 (p0) REVERT: A 756 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7295 (m-40) REVERT: A 757 CYS cc_start: 0.7799 (p) cc_final: 0.7521 (p) REVERT: A 812 TRP cc_start: 0.6264 (OUTLIER) cc_final: 0.5703 (p-90) REVERT: F 109 ARG cc_start: 0.4569 (mtm180) cc_final: 0.4061 (mtm180) outliers start: 32 outliers final: 13 residues processed: 141 average time/residue: 0.1835 time to fit residues: 35.4998 Evaluate side-chains 123 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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: 4.9990 chunk 14 optimal weight: 0.0060 chunk 46 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 78 optimal weight: 0.0570 chunk 7 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.5716 ------------------------------------------------------------------------------- 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 A 437 ASN A 740 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.132260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.110873 restraints weight = 12784.112| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.99 r_work: 0.3285 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7408 Z= 0.208 Angle : 0.627 10.753 10050 Z= 0.316 Chirality : 0.044 0.217 1166 Planarity : 0.004 0.047 1271 Dihedral : 3.998 22.361 986 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.66 % Allowed : 12.93 % Favored : 83.41 % 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: -0.87 (0.28), residues: 916 helix: 2.06 (0.36), residues: 214 sheet: -1.23 (0.37), residues: 192 loop : -1.52 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 539 HIS 0.004 0.001 HIS A 256 PHE 0.020 0.001 PHE A 679 TYR 0.018 0.001 TYR A 725 ARG 0.008 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.861 Fit side-chains REVERT: A 215 SER cc_start: 0.9319 (t) cc_final: 0.9028 (p) REVERT: A 412 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7462 (pp) REVERT: A 690 SER cc_start: 0.8384 (p) cc_final: 0.8148 (m) REVERT: A 740 ASN cc_start: 0.5371 (OUTLIER) cc_final: 0.4791 (p0) REVERT: A 756 ASN cc_start: 0.7625 (OUTLIER) cc_final: 0.7325 (m-40) REVERT: A 812 TRP cc_start: 0.6253 (OUTLIER) cc_final: 0.5648 (p-90) REVERT: E 49 SER cc_start: 0.8804 (p) cc_final: 0.8557 (t) REVERT: F 40 MET cc_start: 0.7730 (ptm) cc_final: 0.7188 (ptt) outliers start: 30 outliers final: 17 residues processed: 132 average time/residue: 0.1892 time to fit residues: 33.8726 Evaluate side-chains 121 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 231 ASP 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 60 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.129016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.107298 restraints weight = 12700.823| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.73 r_work: 0.3241 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7408 Z= 0.308 Angle : 0.725 16.837 10050 Z= 0.359 Chirality : 0.046 0.222 1166 Planarity : 0.005 0.052 1271 Dihedral : 4.457 23.274 985 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 4.02 % Allowed : 14.27 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.28), residues: 916 helix: 1.78 (0.36), residues: 217 sheet: -1.41 (0.36), residues: 195 loop : -1.67 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 539 HIS 0.005 0.001 HIS F 68 PHE 0.018 0.002 PHE A 706 TYR 0.016 0.002 TYR A 725 ARG 0.007 0.001 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 215 SER cc_start: 0.9300 (t) cc_final: 0.9000 (p) REVERT: A 412 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7719 (pp) REVERT: A 539 TRP cc_start: 0.8077 (p-90) cc_final: 0.7864 (p-90) REVERT: A 690 SER cc_start: 0.8314 (p) cc_final: 0.8093 (m) REVERT: A 756 ASN cc_start: 0.7664 (m110) cc_final: 0.7298 (m-40) REVERT: A 812 TRP cc_start: 0.6221 (OUTLIER) cc_final: 0.5612 (p-90) REVERT: F 40 MET cc_start: 0.7720 (ptm) cc_final: 0.7300 (ptt) REVERT: F 129 GLU cc_start: 0.8482 (pt0) cc_final: 0.8262 (pt0) outliers start: 33 outliers final: 20 residues processed: 131 average time/residue: 0.2162 time to fit residues: 38.4745 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 : 0.870 ------------------------------------------------------------------------------- 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 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 A residue 812 TRP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 70 optimal weight: 0.0270 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.129722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.108004 restraints weight = 12877.920| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.82 r_work: 0.3250 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7408 Z= 0.243 Angle : 0.665 14.428 10050 Z= 0.329 Chirality : 0.044 0.197 1166 Planarity : 0.004 0.052 1271 Dihedral : 4.232 21.731 985 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.78 % Allowed : 15.00 % 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: -1.06 (0.28), residues: 916 helix: 1.94 (0.37), residues: 214 sheet: -1.41 (0.36), residues: 194 loop : -1.63 (0.26), residues: 508 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 0.012 0.001 PHE A 547 TYR 0.015 0.001 TYR A 725 ARG 0.006 0.000 ARG A 275 *********************** 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 129 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.789 Fit side-chains REVERT: A 242 GLN cc_start: 0.8126 (tt0) cc_final: 0.7882 (tm-30) REVERT: A 412 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7869 (pp) REVERT: A 539 TRP cc_start: 0.7980 (p-90) cc_final: 0.7727 (p-90) REVERT: A 690 SER cc_start: 0.8330 (p) cc_final: 0.8094 (m) REVERT: A 756 ASN cc_start: 0.7613 (OUTLIER) cc_final: 0.7224 (m-40) REVERT: A 812 TRP cc_start: 0.6099 (OUTLIER) cc_final: 0.5525 (p-90) REVERT: F 40 MET cc_start: 0.7700 (ptm) cc_final: 0.7303 (ptt) REVERT: F 129 GLU cc_start: 0.8539 (pt0) cc_final: 0.8324 (pt0) outliers start: 31 outliers final: 20 residues processed: 124 average time/residue: 0.1985 time to fit residues: 32.9410 Evaluate side-chains 119 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain F residue 126 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.0050 chunk 58 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.131007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.109853 restraints weight = 12728.620| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.69 r_work: 0.3284 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4450 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= 0.189 Angle : 0.625 13.171 10050 Z= 0.311 Chirality : 0.043 0.184 1166 Planarity : 0.004 0.049 1271 Dihedral : 4.092 20.760 985 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.05 % Allowed : 15.98 % Favored : 80.98 % 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: 2.01 (0.37), residues: 214 sheet: -1.32 (0.39), residues: 175 loop : -1.60 (0.25), residues: 527 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 0.022 0.001 PHE A 679 TYR 0.013 0.001 TYR A 725 ARG 0.007 0.000 ARG A 275 *********************** 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 124 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.796 Fit side-chains REVERT: A 412 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7626 (pp) REVERT: A 539 TRP cc_start: 0.7964 (p-90) cc_final: 0.7702 (p-90) REVERT: A 550 LEU cc_start: 0.7325 (mt) cc_final: 0.6676 (mp) REVERT: A 690 SER cc_start: 0.8325 (p) cc_final: 0.8097 (m) REVERT: A 756 ASN cc_start: 0.7503 (OUTLIER) cc_final: 0.7119 (m-40) REVERT: F 40 MET cc_start: 0.7668 (ptm) cc_final: 0.7272 (ptt) REVERT: F 129 GLU cc_start: 0.8458 (pt0) cc_final: 0.8248 (pt0) outliers start: 25 outliers final: 18 residues processed: 119 average time/residue: 0.2106 time to fit residues: 33.7371 Evaluate side-chains 117 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 86 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 0.0570 chunk 80 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.9302 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.128592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.107063 restraints weight = 12805.154| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.69 r_work: 0.3240 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7408 Z= 0.278 Angle : 0.701 13.029 10050 Z= 0.348 Chirality : 0.045 0.216 1166 Planarity : 0.004 0.050 1271 Dihedral : 4.380 26.899 985 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.41 % Allowed : 15.98 % 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: -1.06 (0.27), residues: 916 helix: 2.00 (0.36), residues: 208 sheet: -1.42 (0.38), residues: 179 loop : -1.62 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 812 HIS 0.005 0.001 HIS A 256 PHE 0.022 0.001 PHE A 679 TYR 0.019 0.002 TYR A 801 ARG 0.004 0.000 ARG E 97 *********************** 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: 28 poor density : 101 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 242 GLN cc_start: 0.8080 (tt0) cc_final: 0.7841 (tm-30) REVERT: A 412 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7955 (pp) REVERT: A 539 TRP cc_start: 0.8047 (p-90) cc_final: 0.7796 (p-90) REVERT: A 690 SER cc_start: 0.8295 (p) cc_final: 0.8042 (m) REVERT: A 756 ASN cc_start: 0.7605 (m110) cc_final: 0.7203 (m-40) REVERT: E 107 ARG cc_start: 0.8231 (ttm-80) cc_final: 0.7931 (ttm-80) REVERT: F 40 MET cc_start: 0.7692 (ptm) cc_final: 0.7314 (ptt) REVERT: F 109 ARG cc_start: 0.4747 (mtm110) cc_final: 0.4271 (mtm110) REVERT: F 129 GLU cc_start: 0.8502 (pt0) cc_final: 0.8268 (pt0) outliers start: 28 outliers final: 23 residues processed: 123 average time/residue: 0.3997 time to fit residues: 66.4175 Evaluate side-chains 121 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.801 ------------------------------------------------------------------------------- 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 526 THR 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 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 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: 0.7980 chunk 53 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 88 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.130943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.109850 restraints weight = 12886.768| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.48 r_work: 0.3301 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7408 Z= 0.197 Angle : 0.634 12.262 10050 Z= 0.316 Chirality : 0.044 0.169 1166 Planarity : 0.004 0.050 1271 Dihedral : 4.141 23.771 985 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.93 % Allowed : 17.07 % Favored : 80.00 % 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: 2.19 (0.37), residues: 209 sheet: -1.44 (0.38), residues: 177 loop : -1.69 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 812 HIS 0.003 0.001 HIS A 256 PHE 0.022 0.001 PHE A 679 TYR 0.016 0.001 TYR A 725 ARG 0.005 0.000 ARG E 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 122 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.721 Fit side-chains REVERT: A 242 GLN cc_start: 0.8043 (tt0) cc_final: 0.7819 (tm-30) REVERT: A 412 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7939 (pp) REVERT: A 460 ARG cc_start: 0.7107 (mtt180) cc_final: 0.6828 (mtt180) REVERT: A 539 TRP cc_start: 0.7781 (p-90) cc_final: 0.7530 (p-90) REVERT: A 690 SER cc_start: 0.8266 (p) cc_final: 0.7981 (m) REVERT: A 756 ASN cc_start: 0.7501 (OUTLIER) cc_final: 0.7090 (m-40) REVERT: A 814 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8690 (mt) REVERT: E 81 PHE cc_start: 0.6113 (m-10) cc_final: 0.5775 (m-10) REVERT: E 107 ARG cc_start: 0.8186 (ttm-80) cc_final: 0.7909 (ttm-80) REVERT: F 40 MET cc_start: 0.7599 (ptm) cc_final: 0.7222 (ptt) REVERT: F 129 GLU cc_start: 0.8462 (pt0) cc_final: 0.8242 (pt0) outliers start: 24 outliers final: 20 residues processed: 117 average time/residue: 0.2422 time to fit residues: 37.7392 Evaluate side-chains 118 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS 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 526 THR 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 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 48 ILE 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: 0.7980 chunk 8 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.127806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.106440 restraints weight = 13014.976| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.65 r_work: 0.3206 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 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 : 0.005 0.046 7408 Z= 0.360 Angle : 0.754 12.963 10050 Z= 0.374 Chirality : 0.048 0.176 1166 Planarity : 0.005 0.051 1271 Dihedral : 4.643 23.291 985 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 3.05 % Allowed : 17.07 % Favored : 79.88 % 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: -1.25 (0.27), residues: 916 helix: 1.79 (0.36), residues: 215 sheet: -1.43 (0.39), residues: 174 loop : -1.82 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 812 HIS 0.007 0.001 HIS A 209 PHE 0.022 0.002 PHE A 679 TYR 0.015 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 124 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.919 Fit side-chains REVERT: A 242 GLN cc_start: 0.8097 (tt0) cc_final: 0.7815 (tm-30) REVERT: A 412 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8123 (pp) REVERT: A 460 ARG cc_start: 0.7101 (mtt180) cc_final: 0.6789 (mtt180) REVERT: A 476 CYS cc_start: 0.6916 (m) cc_final: 0.6669 (p) REVERT: A 539 TRP cc_start: 0.7947 (p-90) cc_final: 0.7698 (p-90) REVERT: A 690 SER cc_start: 0.8324 (p) cc_final: 0.8003 (m) REVERT: A 756 ASN cc_start: 0.7621 (m110) cc_final: 0.7075 (m-40) REVERT: A 814 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8674 (mt) REVERT: E 81 PHE cc_start: 0.6376 (m-10) cc_final: 0.5990 (m-10) REVERT: E 107 ARG cc_start: 0.8273 (ttm-80) cc_final: 0.7979 (ttm-80) REVERT: F 40 MET cc_start: 0.7739 (ptm) cc_final: 0.7351 (ptt) REVERT: F 129 GLU cc_start: 0.8491 (pt0) cc_final: 0.8278 (pt0) outliers start: 25 outliers final: 22 residues processed: 118 average time/residue: 0.2198 time to fit residues: 34.6839 Evaluate side-chains 122 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 239 GLU Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 526 THR 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 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 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 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: 0.9980 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 31 optimal weight: 0.0040 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS A 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.130922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.109583 restraints weight = 12867.298| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.41 r_work: 0.3307 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7408 Z= 0.187 Angle : 0.627 12.006 10050 Z= 0.313 Chirality : 0.044 0.146 1166 Planarity : 0.004 0.050 1271 Dihedral : 4.181 21.570 985 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.80 % Allowed : 17.32 % Favored : 79.88 % 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: -1.06 (0.27), residues: 916 helix: 2.17 (0.37), residues: 209 sheet: -1.43 (0.38), residues: 173 loop : -1.71 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 812 HIS 0.003 0.001 HIS A 219 PHE 0.022 0.001 PHE A 679 TYR 0.014 0.001 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: 5197.34 seconds wall clock time: 92 minutes 2.95 seconds (5522.95 seconds total)