Starting phenix.real_space_refine on Fri Aug 22 19:24:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wvy_37876/08_2025/8wvy_37876.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wvy_37876/08_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_37876/08_2025/8wvy_37876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wvy_37876/08_2025/8wvy_37876.map" model { file = "/net/cci-nas-00/data/ceres_data/8wvy_37876/08_2025/8wvy_37876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wvy_37876/08_2025/8wvy_37876.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.87, per 1000 atoms: 0.26 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: 0.42 Conformation dependent library (CDL) restraints added in 284.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.19 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: 1.10 Time building geometry restraints manager: 0.57 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: 4.100 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: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.820 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.448 7425 Z= 1.028 Angle : 1.372 21.006 10084 Z= 0.987 Chirality : 0.050 0.325 1166 Planarity : 0.007 0.065 1271 Dihedral : 8.911 59.974 2669 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.80 % Allowed : 4.51 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A 40 TYR 0.018 0.001 TYR F 120 PHE 0.008 0.001 PHE A 696 TRP 0.022 0.001 TRP A 812 HIS 0.003 0.000 HIS A 683 Details of bonding type rmsd covalent geometry : bond 0.01253 ( 7408) covalent geometry : angle 1.33618 (10050) SS BOND : bond 0.18129 ( 17) SS BOND : angle 5.50278 ( 34) hydrogen bonds : bond 0.26756 ( 223) hydrogen bonds : angle 7.14129 ( 651) *********************** 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 : 0.276 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: 0.7699 (mt0) REVERT: A 212 LYS cc_start: 0.7471 (mttt) cc_final: 0.7268 (mtmt) REVERT: A 215 SER cc_start: 0.8933 (t) cc_final: 0.8373 (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: 0.6889 (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: 0.7325 (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: 0.6916 (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: 0.0897 time to fit residues: 23.7512 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 : 0.274 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0570 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.0060 chunk 74 optimal weight: 2.9990 overall best weight: 0.5314 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.135601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.114568 restraints weight = 12830.449| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.63 r_work: 0.3355 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7425 Z= 0.142 Angle : 0.637 9.412 10084 Z= 0.323 Chirality : 0.044 0.176 1166 Planarity : 0.004 0.046 1271 Dihedral : 5.260 47.363 999 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.17 % Allowed : 10.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.28), residues: 916 helix: 1.85 (0.36), residues: 214 sheet: -1.12 (0.39), residues: 190 loop : -1.41 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 109 TYR 0.019 0.002 TYR A 801 PHE 0.021 0.001 PHE A 547 TRP 0.016 0.002 TRP A 812 HIS 0.009 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7408) covalent geometry : angle 0.62935 (10050) SS BOND : bond 0.00442 ( 17) SS BOND : angle 1.81508 ( 34) hydrogen bonds : bond 0.06094 ( 223) hydrogen bonds : angle 4.81648 ( 651) *********************** 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 166 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 SER cc_start: 0.9275 (t) cc_final: 0.9020 (p) REVERT: A 539 TRP cc_start: 0.8115 (p-90) cc_final: 0.7860 (p-90) REVERT: A 690 SER cc_start: 0.8420 (p) cc_final: 0.8194 (m) REVERT: A 740 ASN cc_start: 0.5070 (OUTLIER) cc_final: 0.4847 (p0) REVERT: A 756 ASN cc_start: 0.7752 (m110) cc_final: 0.7282 (m-40) REVERT: A 808 PHE cc_start: 0.6312 (m-80) cc_final: 0.6057 (m-10) REVERT: E 73 SER cc_start: 0.8185 (p) cc_final: 0.7908 (m) REVERT: F 47 SER cc_start: 0.8252 (m) cc_final: 0.7633 (p) REVERT: F 109 ARG cc_start: 0.4525 (mtm180) cc_final: 0.4116 (mtm180) outliers start: 26 outliers final: 13 residues processed: 162 average time/residue: 0.0750 time to fit residues: 16.5683 Evaluate side-chains 131 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 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 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 2 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 89 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 87 GLN A 116 GLN E 127 HIS F 42 HIS F 43 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.129586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.108170 restraints weight = 12513.641| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.89 r_work: 0.3238 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7425 Z= 0.222 Angle : 0.755 14.235 10084 Z= 0.378 Chirality : 0.048 0.288 1166 Planarity : 0.005 0.052 1271 Dihedral : 4.703 38.361 987 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 4.39 % Allowed : 12.80 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.28), residues: 916 helix: 1.91 (0.36), residues: 210 sheet: -1.39 (0.36), residues: 192 loop : -1.62 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 275 TYR 0.024 0.002 TYR A 725 PHE 0.020 0.002 PHE A 706 TRP 0.014 0.002 TRP A 602 HIS 0.016 0.002 HIS E 127 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 7408) covalent geometry : angle 0.73977 (10050) SS BOND : bond 0.00535 ( 17) SS BOND : angle 2.71391 ( 34) hydrogen bonds : bond 0.06583 ( 223) hydrogen bonds : angle 4.72161 ( 651) *********************** 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 150 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 SER cc_start: 0.9318 (t) cc_final: 0.9012 (p) REVERT: A 412 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7514 (pp) REVERT: A 690 SER cc_start: 0.8396 (p) cc_final: 0.8103 (m) REVERT: A 756 ASN cc_start: 0.7705 (OUTLIER) cc_final: 0.7361 (m-40) REVERT: A 757 CYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7535 (p) REVERT: A 812 TRP cc_start: 0.6398 (OUTLIER) cc_final: 0.5818 (p-90) REVERT: F 109 ARG cc_start: 0.4689 (mtm110) cc_final: 0.4237 (mtm180) outliers start: 36 outliers final: 16 residues processed: 140 average time/residue: 0.0653 time to fit residues: 12.6985 Evaluate side-chains 124 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 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 618 CYS 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 812 TRP Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 60 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 36 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 ASN A 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.130593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.108874 restraints weight = 12847.484| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.93 r_work: 0.3256 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7425 Z= 0.160 Angle : 0.700 14.833 10084 Z= 0.347 Chirality : 0.045 0.234 1166 Planarity : 0.004 0.052 1271 Dihedral : 4.340 31.849 986 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.66 % Allowed : 13.90 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.28), residues: 916 helix: 2.03 (0.37), residues: 210 sheet: -1.46 (0.36), residues: 197 loop : -1.56 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 275 TYR 0.018 0.002 TYR A 725 PHE 0.017 0.001 PHE A 679 TRP 0.013 0.002 TRP A 539 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 7408) covalent geometry : angle 0.68121 (10050) SS BOND : bond 0.00517 ( 17) SS BOND : angle 2.86094 ( 34) hydrogen bonds : bond 0.05404 ( 223) hydrogen bonds : angle 4.57227 ( 651) *********************** 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 141 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 215 SER cc_start: 0.9309 (t) cc_final: 0.9005 (p) REVERT: A 242 GLN cc_start: 0.8110 (tt0) cc_final: 0.7883 (tm-30) REVERT: A 412 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7603 (pp) REVERT: A 690 SER cc_start: 0.8383 (p) cc_final: 0.8153 (m) REVERT: A 756 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.7185 (m-40) REVERT: A 812 TRP cc_start: 0.6308 (OUTLIER) cc_final: 0.5739 (p-90) REVERT: E 49 SER cc_start: 0.8875 (p) cc_final: 0.8570 (t) outliers start: 30 outliers final: 14 residues processed: 135 average time/residue: 0.0897 time to fit residues: 16.2924 Evaluate side-chains 122 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 231 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 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 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 78 optimal weight: 0.0670 chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 0.0010 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.0870 chunk 23 optimal weight: 0.0470 chunk 40 optimal weight: 0.0060 chunk 90 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 44 optimal weight: 0.0060 overall best weight: 0.0254 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.140989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.119987 restraints weight = 12933.810| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.69 r_work: 0.3394 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 7425 Z= 0.099 Angle : 0.565 9.190 10084 Z= 0.285 Chirality : 0.041 0.184 1166 Planarity : 0.004 0.047 1271 Dihedral : 3.708 22.730 985 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.32 % Allowed : 15.00 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.28), residues: 916 helix: 2.19 (0.36), residues: 215 sheet: -1.24 (0.36), residues: 197 loop : -1.39 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 275 TYR 0.013 0.001 TYR A 725 PHE 0.022 0.001 PHE A 679 TRP 0.013 0.001 TRP A 539 HIS 0.003 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 7408) covalent geometry : angle 0.55194 (10050) SS BOND : bond 0.00399 ( 17) SS BOND : angle 2.13178 ( 34) hydrogen bonds : bond 0.03424 ( 223) hydrogen bonds : angle 4.18479 ( 651) *********************** 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 136 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7757 (t70) cc_final: 0.7489 (p0) REVERT: A 215 SER cc_start: 0.9226 (t) cc_final: 0.8980 (p) REVERT: A 412 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7455 (pp) REVERT: A 460 ARG cc_start: 0.7006 (mtt180) cc_final: 0.6661 (mtt180) REVERT: A 539 TRP cc_start: 0.7802 (p-90) cc_final: 0.7513 (p-90) REVERT: A 690 SER cc_start: 0.8399 (p) cc_final: 0.8115 (m) REVERT: A 756 ASN cc_start: 0.7329 (OUTLIER) cc_final: 0.6998 (m-40) REVERT: E 81 PHE cc_start: 0.6147 (m-10) cc_final: 0.5789 (m-10) REVERT: F 40 MET cc_start: 0.7615 (ptm) cc_final: 0.7192 (ptt) outliers start: 19 outliers final: 7 residues processed: 132 average time/residue: 0.0778 time to fit residues: 13.9935 Evaluate side-chains 113 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 756 ASN Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 80 SER 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 7 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.1980 chunk 63 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 14 optimal weight: 0.0870 chunk 19 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.131473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.110332 restraints weight = 12870.524| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.67 r_work: 0.3286 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7425 Z= 0.149 Angle : 0.661 9.411 10084 Z= 0.329 Chirality : 0.044 0.191 1166 Planarity : 0.004 0.044 1271 Dihedral : 4.016 21.215 985 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.44 % Allowed : 15.49 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.28), residues: 916 helix: 2.08 (0.36), residues: 215 sheet: -1.37 (0.38), residues: 178 loop : -1.46 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 275 TYR 0.028 0.002 TYR A 801 PHE 0.012 0.001 PHE A 696 TRP 0.022 0.002 TRP A 812 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 7408) covalent geometry : angle 0.64410 (10050) SS BOND : bond 0.00568 ( 17) SS BOND : angle 2.61193 ( 34) hydrogen bonds : bond 0.04817 ( 223) hydrogen bonds : angle 4.38086 ( 651) *********************** 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 125 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 215 SER cc_start: 0.9291 (t) cc_final: 0.9026 (p) REVERT: A 412 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7588 (pp) REVERT: A 460 ARG cc_start: 0.6974 (mtt180) cc_final: 0.6678 (mtt180) REVERT: A 539 TRP cc_start: 0.7970 (p-90) cc_final: 0.7706 (p-90) REVERT: A 690 SER cc_start: 0.8390 (p) cc_final: 0.8080 (m) REVERT: A 745 MET cc_start: 0.8345 (mmm) cc_final: 0.8033 (mmm) REVERT: A 756 ASN cc_start: 0.7434 (m110) cc_final: 0.7051 (m-40) REVERT: E 81 PHE cc_start: 0.6149 (m-10) cc_final: 0.5828 (m-10) REVERT: F 40 MET cc_start: 0.7746 (ptm) cc_final: 0.7323 (ptt) outliers start: 20 outliers final: 13 residues processed: 120 average time/residue: 0.0670 time to fit residues: 11.0930 Evaluate side-chains 111 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 239 GLU 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 88 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3886 r_free = 0.3886 target = 0.131504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.109997 restraints weight = 12848.418| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.72 r_work: 0.3276 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7425 Z= 0.129 Angle : 0.619 8.804 10084 Z= 0.310 Chirality : 0.043 0.181 1166 Planarity : 0.004 0.042 1271 Dihedral : 3.979 20.156 985 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.44 % Allowed : 15.37 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.28), residues: 916 helix: 2.10 (0.36), residues: 215 sheet: -1.42 (0.38), residues: 181 loop : -1.49 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 97 TYR 0.018 0.001 TYR A 801 PHE 0.010 0.001 PHE A 547 TRP 0.017 0.001 TRP A 812 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7408) covalent geometry : angle 0.60505 (10050) SS BOND : bond 0.00450 ( 17) SS BOND : angle 2.32257 ( 34) hydrogen bonds : bond 0.04592 ( 223) hydrogen bonds : angle 4.30889 ( 651) *********************** 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: 20 poor density : 104 time to evaluate : 0.339 Fit side-chains REVERT: A 215 SER cc_start: 0.9295 (t) cc_final: 0.9023 (p) REVERT: A 412 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7548 (pp) REVERT: A 437 ASN cc_start: 0.8352 (t0) cc_final: 0.7987 (t0) REVERT: A 476 CYS cc_start: 0.6876 (m) cc_final: 0.6665 (p) REVERT: A 539 TRP cc_start: 0.7993 (p-90) cc_final: 0.7710 (p-90) REVERT: A 690 SER cc_start: 0.8315 (p) cc_final: 0.8041 (m) REVERT: A 756 ASN cc_start: 0.7452 (m110) cc_final: 0.7079 (m-40) REVERT: E 81 PHE cc_start: 0.6168 (m-10) cc_final: 0.5884 (m-10) REVERT: F 40 MET cc_start: 0.7854 (ptm) cc_final: 0.7430 (ptt) outliers start: 20 outliers final: 14 residues processed: 119 average time/residue: 0.0839 time to fit residues: 13.4128 Evaluate side-chains 114 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 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 E residue 119 THR 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 18 optimal weight: 2.9990 chunk 23 optimal weight: 0.0000 chunk 54 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 84 optimal weight: 0.0980 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.136660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.114906 restraints weight = 12925.714| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.52 r_work: 0.3332 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7425 Z= 0.109 Angle : 0.599 10.098 10084 Z= 0.300 Chirality : 0.042 0.172 1166 Planarity : 0.004 0.042 1271 Dihedral : 3.838 19.983 985 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.07 % Allowed : 16.34 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.28), residues: 916 helix: 2.23 (0.36), residues: 216 sheet: -1.30 (0.39), residues: 176 loop : -1.48 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 97 TYR 0.018 0.001 TYR A 801 PHE 0.009 0.001 PHE A 547 TRP 0.015 0.001 TRP A 812 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 7408) covalent geometry : angle 0.58639 (10050) SS BOND : bond 0.00366 ( 17) SS BOND : angle 2.18964 ( 34) hydrogen bonds : bond 0.04079 ( 223) hydrogen bonds : angle 4.25642 ( 651) *********************** 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 119 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.274 Fit side-chains REVERT: A 215 SER cc_start: 0.9276 (t) cc_final: 0.8997 (p) REVERT: A 412 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7484 (pp) REVERT: A 460 ARG cc_start: 0.6981 (mtt180) cc_final: 0.6577 (mtt180) REVERT: A 539 TRP cc_start: 0.7945 (p-90) cc_final: 0.7655 (p-90) REVERT: A 550 LEU cc_start: 0.7397 (mt) cc_final: 0.6799 (mp) REVERT: A 690 SER cc_start: 0.8302 (p) cc_final: 0.7947 (m) REVERT: A 756 ASN cc_start: 0.7381 (m110) cc_final: 0.7156 (m-40) REVERT: E 81 PHE cc_start: 0.6192 (m-10) cc_final: 0.5955 (m-10) REVERT: E 107 ARG cc_start: 0.8203 (ttm-80) cc_final: 0.7925 (ttm-80) REVERT: F 40 MET cc_start: 0.7804 (ptm) cc_final: 0.7370 (ptt) outliers start: 17 outliers final: 13 residues processed: 115 average time/residue: 0.0947 time to fit residues: 14.4463 Evaluate side-chains 111 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 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 73 SER 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 15 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 4 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 0.0050 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 0.0870 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.3570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.132717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.111815 restraints weight = 12813.842| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.56 r_work: 0.3333 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7425 Z= 0.105 Angle : 0.584 9.456 10084 Z= 0.290 Chirality : 0.042 0.149 1166 Planarity : 0.004 0.042 1271 Dihedral : 3.743 20.505 985 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.83 % Allowed : 16.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.28), residues: 916 helix: 2.28 (0.36), residues: 216 sheet: -1.32 (0.39), residues: 177 loop : -1.44 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 97 TYR 0.016 0.001 TYR A 801 PHE 0.023 0.001 PHE A 679 TRP 0.014 0.001 TRP A 812 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 7408) covalent geometry : angle 0.57341 (10050) SS BOND : bond 0.00383 ( 17) SS BOND : angle 2.01153 ( 34) hydrogen bonds : bond 0.03867 ( 223) hydrogen bonds : angle 4.19110 ( 651) *********************** 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 115 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.221 Fit side-chains REVERT: A 215 SER cc_start: 0.9263 (t) cc_final: 0.9005 (p) REVERT: A 412 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7749 (pp) REVERT: A 437 ASN cc_start: 0.8183 (t0) cc_final: 0.7801 (t0) REVERT: A 460 ARG cc_start: 0.6984 (mtt180) cc_final: 0.6610 (mtt180) REVERT: A 539 TRP cc_start: 0.7933 (p-90) cc_final: 0.7626 (p-90) REVERT: A 550 LEU cc_start: 0.7443 (mt) cc_final: 0.6812 (mp) REVERT: E 107 ARG cc_start: 0.8232 (ttm-80) cc_final: 0.7946 (ttm-80) REVERT: F 40 MET cc_start: 0.7793 (ptm) cc_final: 0.7395 (ptt) outliers start: 15 outliers final: 12 residues processed: 111 average time/residue: 0.0925 time to fit residues: 13.7566 Evaluate side-chains 111 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 73 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 11 optimal weight: 0.5980 chunk 68 optimal weight: 0.0770 chunk 57 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 74 optimal weight: 0.0570 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.0050 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 overall best weight: 0.2670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.134089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.113192 restraints weight = 12973.238| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.68 r_work: 0.3356 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7425 Z= 0.097 Angle : 0.557 9.546 10084 Z= 0.277 Chirality : 0.041 0.136 1166 Planarity : 0.004 0.042 1271 Dihedral : 3.591 19.108 985 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.83 % Allowed : 16.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.28), residues: 916 helix: 2.40 (0.37), residues: 216 sheet: -1.24 (0.39), residues: 176 loop : -1.39 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 97 TYR 0.014 0.001 TYR A 801 PHE 0.025 0.001 PHE A 679 TRP 0.013 0.001 TRP A 812 HIS 0.004 0.000 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 7408) covalent geometry : angle 0.54879 (10050) SS BOND : bond 0.00367 ( 17) SS BOND : angle 1.71678 ( 34) hydrogen bonds : bond 0.03523 ( 223) hydrogen bonds : angle 4.00856 ( 651) ********************** 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 115 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.180 Fit side-chains REVERT: A 215 SER cc_start: 0.9244 (t) cc_final: 0.9007 (p) REVERT: A 412 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7714 (pp) REVERT: A 474 TRP cc_start: 0.6688 (t-100) cc_final: 0.6448 (t-100) REVERT: A 539 TRP cc_start: 0.7722 (p-90) cc_final: 0.7441 (p-90) REVERT: A 550 LEU cc_start: 0.7421 (mt) cc_final: 0.6786 (mp) REVERT: F 40 MET cc_start: 0.7755 (ptm) cc_final: 0.7363 (ptt) outliers start: 15 outliers final: 11 residues processed: 111 average time/residue: 0.0803 time to fit residues: 12.1139 Evaluate side-chains 107 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 595 THR Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 73 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 22 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 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 219 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.130958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.109726 restraints weight = 12978.858| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.60 r_work: 0.3307 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7425 Z= 0.141 Angle : 0.632 9.360 10084 Z= 0.316 Chirality : 0.043 0.156 1166 Planarity : 0.004 0.042 1271 Dihedral : 3.920 19.121 985 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 1.95 % Allowed : 16.71 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.28), residues: 916 helix: 2.21 (0.36), residues: 212 sheet: -1.24 (0.38), residues: 193 loop : -1.40 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 97 TYR 0.021 0.002 TYR A 801 PHE 0.024 0.001 PHE A 679 TRP 0.031 0.002 TRP A 812 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7408) covalent geometry : angle 0.62134 (10050) SS BOND : bond 0.00446 ( 17) SS BOND : angle 2.11362 ( 34) hydrogen bonds : bond 0.04536 ( 223) hydrogen bonds : angle 4.16239 ( 651) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2033.70 seconds wall clock time: 35 minutes 23.75 seconds (2123.75 seconds total)