Starting phenix.real_space_refine on Wed Sep 17 09:27:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s37_54527/09_2025/9s37_54527.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s37_54527/09_2025/9s37_54527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9s37_54527/09_2025/9s37_54527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s37_54527/09_2025/9s37_54527.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9s37_54527/09_2025/9s37_54527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s37_54527/09_2025/9s37_54527.map" } resolution = 3.94 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= 0.000 sd= 0.011 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 39 5.16 5 C 4739 2.51 5 N 1226 2.21 5 O 1360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7364 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 904 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 901 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 122, 901 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 916 Chain: "D" Number of atoms: 5744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5744 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 36, 'TRANS': 706} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 2.08, per 1000 atoms: 0.28 Number of scatterers: 7364 At special positions: 0 Unit cell: (74.035, 95.03, 172.38, 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 39 16.00 O 1360 8.00 N 1226 7.00 C 4739 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 33 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS D 33 " - pdb=" SG CYS D 43 " distance=2.03 Simple disulfide: pdb=" SG CYS D 339 " - pdb=" SG CYS D 364 " distance=2.03 Simple disulfide: pdb=" SG CYS D 470 " - pdb=" SG CYS D 522 " distance=2.03 Simple disulfide: pdb=" SG CYS D 618 " - pdb=" SG CYS D 693 " distance=2.03 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: 0.49 Conformation dependent library (CDL) restraints added in 332.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1794 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 12 sheets defined 31.2% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 104 through 114 removed outlier: 4.265A pdb=" N LYS B 109 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP B 110 " --> pdb=" O ASP B 107 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N PHE B 111 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG B 112 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN B 113 " --> pdb=" O ASP B 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 175 Processing helix chain 'D' and resid 242 through 247 Processing helix chain 'D' and resid 266 through 270 removed outlier: 4.475A pdb=" N GLY D 270 " --> pdb=" O ALA D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 381 through 386 removed outlier: 3.827A pdb=" N PHE D 385 " --> pdb=" O GLU D 382 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN D 386 " --> pdb=" O GLY D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 472 Processing helix chain 'D' and resid 538 through 566 removed outlier: 4.171A pdb=" N SER D 566 " --> pdb=" O THR D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 601 Processing helix chain 'D' and resid 604 through 615 removed outlier: 3.878A pdb=" N PHE D 608 " --> pdb=" O ARG D 604 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TRP D 611 " --> pdb=" O GLU D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 650 removed outlier: 4.392A pdb=" N LYS D 619 " --> pdb=" O GLY D 615 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU D 630 " --> pdb=" O VAL D 626 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA D 632 " --> pdb=" O SER D 628 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE D 633 " --> pdb=" O SER D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 679 Processing helix chain 'D' and resid 680 through 683 Processing helix chain 'D' and resid 706 through 732 Processing helix chain 'D' and resid 733 through 740 Processing helix chain 'D' and resid 740 through 769 Proline residue: D 762 - end of helix Processing helix chain 'D' and resid 778 through 790 removed outlier: 3.606A pdb=" N PHE D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 805 removed outlier: 3.755A pdb=" N CYS D 795 " --> pdb=" O PRO D 791 " (cutoff:3.500A) Proline residue: D 798 - end of helix Processing helix chain 'D' and resid 805 through 823 removed outlier: 4.054A pdb=" N LYS D 809 " --> pdb=" O ASN D 805 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.071A pdb=" N GLY B 10 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ALA B 126 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 12 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET B 34 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG B 38 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLY B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.071A pdb=" N GLY B 10 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ALA B 126 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 12 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 40 through 44 removed outlier: 3.854A pdb=" N LEU D 158 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR D 183 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'D' and resid 191 through 192 removed outlier: 3.800A pdb=" N ILE D 192 " --> pdb=" O SER D 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 262 through 263 Processing sheet with id=AA8, first strand: chain 'D' and resid 300 through 304 removed outlier: 4.076A pdb=" N LEU D 324 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP D 349 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU D 326 " --> pdb=" O ASP D 349 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER D 351 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN D 373 " --> pdb=" O LEU D 350 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER D 397 " --> pdb=" O LEU D 372 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS D 440 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 379 through 380 Processing sheet with id=AB1, first strand: chain 'A' and resid 451 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 451 through 453 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 478 308 hydrogen bonds defined for protein. 834 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: 1.31 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1187 1.29 - 1.42: 1993 1.42 - 1.55: 4290 1.55 - 1.68: 12 1.68 - 1.81: 53 Bond restraints: 7535 Sorted by residual: bond pdb=" N PRO D 806 " pdb=" CD PRO D 806 " ideal model delta sigma weight residual 1.473 1.337 0.136 1.40e-02 5.10e+03 9.49e+01 bond pdb=" CA LYS A 481 " pdb=" C LYS A 481 " ideal model delta sigma weight residual 1.522 1.637 -0.115 1.34e-02 5.57e+03 7.30e+01 bond pdb=" N PRO D 465 " pdb=" CD PRO D 465 " ideal model delta sigma weight residual 1.473 1.359 0.114 1.40e-02 5.10e+03 6.67e+01 bond pdb=" N PRO D 695 " pdb=" CD PRO D 695 " ideal model delta sigma weight residual 1.473 1.372 0.101 1.40e-02 5.10e+03 5.19e+01 bond pdb=" C LEU D 550 " pdb=" O LEU D 550 " ideal model delta sigma weight residual 1.236 1.162 0.074 1.15e-02 7.56e+03 4.12e+01 ... (remaining 7530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.36: 10093 5.36 - 10.71: 127 10.71 - 16.07: 20 16.07 - 21.43: 3 21.43 - 26.78: 3 Bond angle restraints: 10246 Sorted by residual: angle pdb=" O SER D 629 " pdb=" C SER D 629 " pdb=" N GLU D 630 " ideal model delta sigma weight residual 122.12 95.34 26.78 1.06e+00 8.90e-01 6.38e+02 angle pdb=" CA SER D 629 " pdb=" C SER D 629 " pdb=" N GLU D 630 " ideal model delta sigma weight residual 117.30 143.27 -25.97 1.16e+00 7.43e-01 5.01e+02 angle pdb=" C SER D 629 " pdb=" N GLU D 630 " pdb=" CA GLU D 630 " ideal model delta sigma weight residual 120.58 145.27 -24.69 1.71e+00 3.42e-01 2.08e+02 angle pdb=" N THR D 701 " pdb=" CA THR D 701 " pdb=" CB THR D 701 " ideal model delta sigma weight residual 111.20 93.13 18.07 1.41e+00 5.03e-01 1.64e+02 angle pdb=" N ILE D 781 " pdb=" CA ILE D 781 " pdb=" C ILE D 781 " ideal model delta sigma weight residual 110.36 123.76 -13.40 1.05e+00 9.07e-01 1.63e+02 ... (remaining 10241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3890 17.94 - 35.89: 425 35.89 - 53.83: 113 53.83 - 71.78: 24 71.78 - 89.72: 11 Dihedral angle restraints: 4463 sinusoidal: 1687 harmonic: 2776 Sorted by residual: dihedral pdb=" N THR D 701 " pdb=" C THR D 701 " pdb=" CA THR D 701 " pdb=" CB THR D 701 " ideal model delta harmonic sigma weight residual 123.40 99.67 23.73 0 2.50e+00 1.60e-01 9.01e+01 dihedral pdb=" CB CYS D 339 " pdb=" SG CYS D 339 " pdb=" SG CYS D 364 " pdb=" CB CYS D 364 " ideal model delta sinusoidal sigma weight residual -86.00 -162.52 76.52 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" C THR D 701 " pdb=" N THR D 701 " pdb=" CA THR D 701 " pdb=" CB THR D 701 " ideal model delta harmonic sigma weight residual -122.00 -101.43 -20.57 0 2.50e+00 1.60e-01 6.77e+01 ... (remaining 4460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 1118 0.136 - 0.272: 52 0.272 - 0.408: 9 0.408 - 0.544: 2 0.544 - 0.680: 3 Chirality restraints: 1184 Sorted by residual: chirality pdb=" CA ASN A 489 " pdb=" N ASN A 489 " pdb=" C ASN A 489 " pdb=" CB ASN A 489 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA SER D 461 " pdb=" N SER D 461 " pdb=" C SER D 461 " pdb=" CB SER D 461 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.90e+00 chirality pdb=" CA LYS A 481 " pdb=" N LYS A 481 " pdb=" C LYS A 481 " pdb=" CB LYS A 481 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.51e+00 ... (remaining 1181 not shown) Planarity restraints: 1303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 135 " -0.922 9.50e-02 1.11e+02 4.13e-01 1.04e+02 pdb=" NE ARG D 135 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG D 135 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG D 135 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG D 135 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 444 " -0.510 9.50e-02 1.11e+02 2.28e-01 3.19e+01 pdb=" NE ARG A 444 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 444 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 444 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 444 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 499 " -0.022 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" C TYR A 499 " 0.080 2.00e-02 2.50e+03 pdb=" O TYR A 499 " -0.029 2.00e-02 2.50e+03 pdb=" N TYR A 500 " -0.028 2.00e-02 2.50e+03 ... (remaining 1300 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2542 2.84 - 3.36: 6778 3.36 - 3.87: 11674 3.87 - 4.39: 12445 4.39 - 4.90: 21668 Nonbonded interactions: 55107 Sorted by model distance: nonbonded pdb=" O ASP D 649 " pdb=" OD1 ASP D 649 " model vdw 2.330 3.040 nonbonded pdb=" N GLU B 44 " pdb=" OE1 GLU B 44 " model vdw 2.371 3.120 nonbonded pdb=" N GLU D 686 " pdb=" OE1 GLU D 686 " model vdw 2.413 3.120 nonbonded pdb=" N TYR A 499 " pdb=" O TYR A 499 " model vdw 2.439 2.496 nonbonded pdb=" O GLN D 60 " pdb=" N GLU D 84 " model vdw 2.440 3.120 ... (remaining 55102 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.690 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.680 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 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 : 0.006 0.136 7540 Z= 0.399 Angle : 1.432 26.782 10256 Z= 0.962 Chirality : 0.077 0.680 1184 Planarity : 0.014 0.413 1303 Dihedral : 16.803 89.719 2654 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.54 % Favored : 95.35 % Rotamer: Outliers : 2.12 % Allowed : 25.97 % Favored : 71.91 % Cbeta Deviations : 1.34 % 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: -0.35 (0.27), residues: 948 helix: 0.98 (0.33), residues: 254 sheet: 0.11 (0.39), residues: 180 loop : -0.98 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 135 TYR 0.010 0.001 TYR A 485 PHE 0.011 0.001 PHE D 576 TRP 0.006 0.001 TRP D 602 HIS 0.007 0.001 HIS D 293 Details of bonding type rmsd covalent geometry : bond 0.00589 ( 7535) covalent geometry : angle 1.43123 (10246) SS BOND : bond 0.00249 ( 5) SS BOND : angle 1.72918 ( 10) hydrogen bonds : bond 0.13693 ( 296) hydrogen bonds : angle 5.71728 ( 834) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.338 Fit side-chains REVERT: D 71 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8329 (pp30) REVERT: D 584 ASN cc_start: 0.8532 (m110) cc_final: 0.8201 (m-40) REVERT: D 759 PHE cc_start: 0.9530 (m-10) cc_final: 0.9135 (m-80) REVERT: A 468 SER cc_start: 0.9292 (OUTLIER) cc_final: 0.9088 (m) REVERT: A 479 ASN cc_start: 0.9474 (p0) cc_final: 0.9104 (t0) outliers start: 17 outliers final: 7 residues processed: 92 average time/residue: 0.0685 time to fit residues: 9.3326 Evaluate side-chains 72 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain D residue 71 GLN Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain A residue 468 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.0060 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.071019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.049972 restraints weight = 41490.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.051972 restraints weight = 20707.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.053433 restraints weight = 13319.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.054327 restraints weight = 9798.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.055086 restraints weight = 7951.610| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7540 Z= 0.130 Angle : 0.623 10.794 10256 Z= 0.312 Chirality : 0.043 0.178 1184 Planarity : 0.004 0.063 1303 Dihedral : 5.512 58.055 1031 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.00 % Allowed : 25.09 % Favored : 70.91 % 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: 0.26 (0.27), residues: 948 helix: 1.91 (0.34), residues: 255 sheet: 0.28 (0.39), residues: 178 loop : -0.77 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 135 TYR 0.011 0.001 TYR A 500 PHE 0.022 0.001 PHE D 759 TRP 0.007 0.001 TRP A 442 HIS 0.003 0.001 HIS D 209 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7535) covalent geometry : angle 0.62144 (10246) SS BOND : bond 0.00232 ( 5) SS BOND : angle 1.44601 ( 10) hydrogen bonds : bond 0.05161 ( 296) hydrogen bonds : angle 4.66664 ( 834) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 0.314 Fit side-chains REVERT: D 71 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8344 (pp30) REVERT: D 278 HIS cc_start: 0.8101 (OUTLIER) cc_final: 0.7821 (m170) REVERT: D 543 LEU cc_start: 0.9203 (mt) cc_final: 0.8772 (pp) REVERT: D 584 ASN cc_start: 0.8520 (m110) cc_final: 0.8106 (t0) REVERT: D 668 LEU cc_start: 0.9670 (OUTLIER) cc_final: 0.9469 (pp) REVERT: D 796 LEU cc_start: 0.9311 (mm) cc_final: 0.8668 (mm) REVERT: A 479 ASN cc_start: 0.9550 (p0) cc_final: 0.9106 (t0) REVERT: A 491 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8274 (pp) REVERT: A 498 MET cc_start: 0.9060 (tpp) cc_final: 0.8556 (tpp) outliers start: 32 outliers final: 14 residues processed: 97 average time/residue: 0.0597 time to fit residues: 9.0564 Evaluate side-chains 82 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain D residue 71 GLN Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 491 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 7 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 342 GLN ** D 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 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 = 0.3248 r_free = 0.3248 target = 0.068533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.048393 restraints weight = 28842.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.049985 restraints weight = 16858.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.051166 restraints weight = 11770.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.051793 restraints weight = 9182.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.052466 restraints weight = 7823.546| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7540 Z= 0.216 Angle : 0.672 10.322 10256 Z= 0.340 Chirality : 0.044 0.167 1184 Planarity : 0.004 0.049 1303 Dihedral : 5.066 50.638 1022 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.62 % Allowed : 25.84 % Favored : 69.54 % 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: 0.27 (0.28), residues: 948 helix: 2.10 (0.34), residues: 251 sheet: 0.22 (0.39), residues: 182 loop : -0.83 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 135 TYR 0.011 0.001 TYR A 500 PHE 0.011 0.001 PHE D 670 TRP 0.009 0.001 TRP B 36 HIS 0.006 0.001 HIS D 209 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 7535) covalent geometry : angle 0.67111 (10246) SS BOND : bond 0.00512 ( 5) SS BOND : angle 1.50538 ( 10) hydrogen bonds : bond 0.05910 ( 296) hydrogen bonds : angle 4.77580 ( 834) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 63 time to evaluate : 0.280 Fit side-chains REVERT: D 71 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8322 (pp30) REVERT: D 419 ASP cc_start: 0.8224 (t0) cc_final: 0.8017 (t0) REVERT: D 543 LEU cc_start: 0.9170 (mt) cc_final: 0.8782 (pp) REVERT: D 584 ASN cc_start: 0.8611 (m110) cc_final: 0.8109 (t0) REVERT: D 593 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7672 (tt) REVERT: D 634 PHE cc_start: 0.8880 (m-10) cc_final: 0.8526 (m-10) REVERT: A 479 ASN cc_start: 0.9550 (p0) cc_final: 0.9103 (t0) REVERT: A 491 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8562 (mp) outliers start: 37 outliers final: 24 residues processed: 94 average time/residue: 0.0600 time to fit residues: 8.7700 Evaluate side-chains 87 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain D residue 71 GLN Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 670 PHE Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 491 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 32 optimal weight: 0.7980 chunk 80 optimal weight: 0.0870 chunk 72 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 39 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.071055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.049454 restraints weight = 51178.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.051623 restraints weight = 23328.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.053187 restraints weight = 14382.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.054243 restraints weight = 10323.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.055015 restraints weight = 8159.546| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7540 Z= 0.108 Angle : 0.601 10.808 10256 Z= 0.292 Chirality : 0.042 0.165 1184 Planarity : 0.003 0.044 1303 Dihedral : 4.687 50.265 1022 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.75 % Allowed : 26.47 % Favored : 69.79 % 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: 0.45 (0.28), residues: 948 helix: 2.22 (0.33), residues: 250 sheet: 0.43 (0.40), residues: 178 loop : -0.73 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 135 TYR 0.008 0.001 TYR A 500 PHE 0.019 0.001 PHE D 759 TRP 0.009 0.001 TRP A 442 HIS 0.002 0.000 HIS D 209 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 7535) covalent geometry : angle 0.60021 (10246) SS BOND : bond 0.00171 ( 5) SS BOND : angle 1.17230 ( 10) hydrogen bonds : bond 0.04482 ( 296) hydrogen bonds : angle 4.46063 ( 834) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: D 71 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8812 (pp30) REVERT: D 278 HIS cc_start: 0.7997 (OUTLIER) cc_final: 0.7756 (m170) REVERT: D 419 ASP cc_start: 0.8180 (t0) cc_final: 0.7915 (t0) REVERT: D 543 LEU cc_start: 0.9138 (mt) cc_final: 0.8744 (pp) REVERT: D 584 ASN cc_start: 0.8499 (m110) cc_final: 0.8159 (m-40) REVERT: D 668 LEU cc_start: 0.9658 (OUTLIER) cc_final: 0.9455 (pp) REVERT: A 479 ASN cc_start: 0.9555 (p0) cc_final: 0.9225 (t0) REVERT: A 498 MET cc_start: 0.9093 (tpp) cc_final: 0.8669 (tpp) outliers start: 30 outliers final: 22 residues processed: 95 average time/residue: 0.0610 time to fit residues: 8.8484 Evaluate side-chains 90 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 71 GLN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 725 TYR Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 483 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 92 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 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 = 0.3243 r_free = 0.3243 target = 0.068394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.048186 restraints weight = 29329.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.049801 restraints weight = 17187.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.051006 restraints weight = 11990.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.051724 restraints weight = 9328.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.052334 restraints weight = 7876.662| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7540 Z= 0.215 Angle : 0.696 14.102 10256 Z= 0.341 Chirality : 0.044 0.172 1184 Planarity : 0.004 0.037 1303 Dihedral : 5.002 46.758 1022 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 5.24 % Allowed : 25.59 % Favored : 69.16 % 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: 0.35 (0.28), residues: 948 helix: 2.07 (0.33), residues: 257 sheet: 0.23 (0.39), residues: 186 loop : -0.75 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 504 TYR 0.010 0.001 TYR A 500 PHE 0.030 0.001 PHE D 759 TRP 0.008 0.001 TRP B 36 HIS 0.006 0.001 HIS D 209 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 7535) covalent geometry : angle 0.69492 (10246) SS BOND : bond 0.00442 ( 5) SS BOND : angle 1.41452 ( 10) hydrogen bonds : bond 0.05654 ( 296) hydrogen bonds : angle 4.73274 ( 834) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 63 time to evaluate : 0.296 Fit side-chains REVERT: B 93 MET cc_start: 0.8869 (tpp) cc_final: 0.8658 (tpp) REVERT: D 62 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9275 (tt) REVERT: D 71 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8800 (pp30) REVERT: D 419 ASP cc_start: 0.8179 (t0) cc_final: 0.7852 (t0) REVERT: D 543 LEU cc_start: 0.9167 (mt) cc_final: 0.8776 (pp) REVERT: D 546 TRP cc_start: 0.7417 (OUTLIER) cc_final: 0.6941 (m-10) REVERT: D 584 ASN cc_start: 0.8544 (m110) cc_final: 0.8207 (m-40) REVERT: D 593 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7614 (tt) REVERT: D 796 LEU cc_start: 0.9392 (mm) cc_final: 0.9120 (mm) REVERT: A 479 ASN cc_start: 0.9577 (p0) cc_final: 0.9258 (t0) outliers start: 42 outliers final: 29 residues processed: 98 average time/residue: 0.0667 time to fit residues: 10.1336 Evaluate side-chains 93 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 60 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 71 GLN Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 546 TRP Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 778 SER Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 483 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 89 optimal weight: 10.0000 chunk 53 optimal weight: 0.0470 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 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 = 0.3237 r_free = 0.3237 target = 0.068088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.046323 restraints weight = 52921.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.048452 restraints weight = 24655.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.049905 restraints weight = 15383.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.050984 restraints weight = 11095.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.051631 restraints weight = 8855.911| |-----------------------------------------------------------------------------| r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7540 Z= 0.218 Angle : 0.698 11.429 10256 Z= 0.343 Chirality : 0.044 0.169 1184 Planarity : 0.004 0.035 1303 Dihedral : 5.252 59.730 1022 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 5.37 % Allowed : 26.34 % Favored : 68.29 % 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: 0.21 (0.27), residues: 948 helix: 2.00 (0.33), residues: 257 sheet: 0.17 (0.39), residues: 180 loop : -0.86 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 135 TYR 0.009 0.001 TYR A 500 PHE 0.031 0.001 PHE D 759 TRP 0.023 0.001 TRP A 442 HIS 0.006 0.001 HIS D 209 Details of bonding type rmsd covalent geometry : bond 0.00505 ( 7535) covalent geometry : angle 0.69754 (10246) SS BOND : bond 0.00505 ( 5) SS BOND : angle 1.35634 ( 10) hydrogen bonds : bond 0.05712 ( 296) hydrogen bonds : angle 4.78348 ( 834) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 64 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: B 93 MET cc_start: 0.8884 (tpp) cc_final: 0.8649 (tpp) REVERT: D 62 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9308 (tt) REVERT: D 71 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8832 (pp30) REVERT: D 419 ASP cc_start: 0.8281 (t0) cc_final: 0.7924 (t0) REVERT: D 543 LEU cc_start: 0.9211 (mt) cc_final: 0.8843 (pp) REVERT: D 546 TRP cc_start: 0.7454 (OUTLIER) cc_final: 0.7024 (m-10) REVERT: D 584 ASN cc_start: 0.8573 (m110) cc_final: 0.8216 (m-40) REVERT: A 498 MET cc_start: 0.9125 (tpp) cc_final: 0.8575 (tpp) outliers start: 42 outliers final: 28 residues processed: 100 average time/residue: 0.0601 time to fit residues: 9.3867 Evaluate side-chains 87 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 56 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 71 GLN Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 546 TRP Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 778 SER Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 483 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 293 HIS ** D 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 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 = 0.3244 r_free = 0.3244 target = 0.068476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.048487 restraints weight = 29222.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.050131 restraints weight = 17273.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.051204 restraints weight = 12091.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.052045 restraints weight = 9481.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.052541 restraints weight = 7934.050| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7540 Z= 0.193 Angle : 0.713 11.857 10256 Z= 0.341 Chirality : 0.044 0.173 1184 Planarity : 0.004 0.032 1303 Dihedral : 4.878 47.695 1020 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 5.24 % Allowed : 26.22 % Favored : 68.54 % 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: 0.19 (0.27), residues: 948 helix: 1.97 (0.33), residues: 257 sheet: 0.13 (0.39), residues: 180 loop : -0.86 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 504 TYR 0.010 0.001 TYR D 725 PHE 0.031 0.001 PHE D 759 TRP 0.009 0.001 TRP B 36 HIS 0.006 0.001 HIS D 209 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 7535) covalent geometry : angle 0.71183 (10246) SS BOND : bond 0.00438 ( 5) SS BOND : angle 1.32165 ( 10) hydrogen bonds : bond 0.05537 ( 296) hydrogen bonds : angle 4.77325 ( 834) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 60 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: B 93 MET cc_start: 0.8889 (tpp) cc_final: 0.8643 (tpp) REVERT: D 71 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8841 (pp30) REVERT: D 419 ASP cc_start: 0.8270 (t0) cc_final: 0.7895 (t0) REVERT: D 543 LEU cc_start: 0.9191 (mt) cc_final: 0.8775 (pp) REVERT: D 546 TRP cc_start: 0.7378 (OUTLIER) cc_final: 0.6955 (m-10) REVERT: D 584 ASN cc_start: 0.8500 (m110) cc_final: 0.8157 (m-40) REVERT: A 498 MET cc_start: 0.9114 (tpp) cc_final: 0.8586 (tpp) outliers start: 41 outliers final: 32 residues processed: 95 average time/residue: 0.0585 time to fit residues: 8.7682 Evaluate side-chains 89 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 55 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 71 GLN Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 546 TRP Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 778 SER Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 483 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 25 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 0.0870 chunk 27 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 293 HIS ** D 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 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 = 0.3264 r_free = 0.3264 target = 0.069398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.047803 restraints weight = 51835.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.049967 restraints weight = 24127.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.051500 restraints weight = 14992.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.052501 restraints weight = 10769.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.053284 restraints weight = 8592.260| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7540 Z= 0.139 Angle : 0.688 13.450 10256 Z= 0.325 Chirality : 0.043 0.167 1184 Planarity : 0.003 0.031 1303 Dihedral : 4.688 45.044 1020 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.37 % Allowed : 26.84 % Favored : 68.79 % 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: 0.27 (0.27), residues: 948 helix: 2.04 (0.34), residues: 257 sheet: 0.17 (0.39), residues: 180 loop : -0.81 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 504 TYR 0.009 0.001 TYR D 725 PHE 0.032 0.001 PHE D 759 TRP 0.010 0.001 TRP A 442 HIS 0.004 0.001 HIS D 209 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7535) covalent geometry : angle 0.68760 (10246) SS BOND : bond 0.00341 ( 5) SS BOND : angle 1.21194 ( 10) hydrogen bonds : bond 0.05071 ( 296) hydrogen bonds : angle 4.65327 ( 834) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: B 93 MET cc_start: 0.8847 (tpp) cc_final: 0.8616 (tpp) REVERT: D 71 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8865 (pp30) REVERT: D 419 ASP cc_start: 0.8203 (t0) cc_final: 0.7851 (t0) REVERT: D 543 LEU cc_start: 0.9176 (mt) cc_final: 0.8763 (pp) REVERT: D 546 TRP cc_start: 0.7334 (OUTLIER) cc_final: 0.6901 (m-10) REVERT: D 584 ASN cc_start: 0.8465 (m110) cc_final: 0.8112 (m-40) REVERT: A 498 MET cc_start: 0.9141 (tpp) cc_final: 0.8662 (tpp) outliers start: 34 outliers final: 26 residues processed: 90 average time/residue: 0.0606 time to fit residues: 8.4946 Evaluate side-chains 86 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 71 GLN Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 546 TRP Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 725 TYR Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 778 SER Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 50 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN D 293 HIS ** D 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.068679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.047703 restraints weight = 40609.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.049656 restraints weight = 20979.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.050973 restraints weight = 13665.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.051969 restraints weight = 10151.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.052564 restraints weight = 8241.432| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7540 Z= 0.175 Angle : 0.733 14.241 10256 Z= 0.343 Chirality : 0.044 0.169 1184 Planarity : 0.003 0.030 1303 Dihedral : 4.722 43.918 1020 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.74 % Allowed : 26.97 % Favored : 68.29 % 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: 0.22 (0.27), residues: 948 helix: 1.92 (0.33), residues: 257 sheet: 0.13 (0.38), residues: 181 loop : -0.79 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 504 TYR 0.011 0.001 TYR D 725 PHE 0.033 0.001 PHE D 576 TRP 0.013 0.001 TRP A 442 HIS 0.010 0.001 HIS D 293 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 7535) covalent geometry : angle 0.73247 (10246) SS BOND : bond 0.00578 ( 5) SS BOND : angle 1.24646 ( 10) hydrogen bonds : bond 0.05323 ( 296) hydrogen bonds : angle 4.73264 ( 834) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 60 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: B 93 MET cc_start: 0.8866 (tpp) cc_final: 0.8639 (tpp) REVERT: D 419 ASP cc_start: 0.8228 (t0) cc_final: 0.7861 (t0) REVERT: D 543 LEU cc_start: 0.9152 (mt) cc_final: 0.8743 (pp) REVERT: D 546 TRP cc_start: 0.7375 (OUTLIER) cc_final: 0.6943 (m-10) REVERT: D 584 ASN cc_start: 0.8506 (m110) cc_final: 0.8138 (m-40) REVERT: A 498 MET cc_start: 0.9162 (tpp) cc_final: 0.8764 (tpp) outliers start: 37 outliers final: 34 residues processed: 91 average time/residue: 0.0562 time to fit residues: 8.1125 Evaluate side-chains 93 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 58 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 546 TRP Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 725 TYR Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 778 SER Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 803 PHE Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 293 HIS ** D 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.068867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.047106 restraints weight = 55723.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.049329 restraints weight = 25171.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.050852 restraints weight = 15412.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.051958 restraints weight = 11034.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.052696 restraints weight = 8711.209| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7540 Z= 0.165 Angle : 0.726 12.427 10256 Z= 0.340 Chirality : 0.044 0.169 1184 Planarity : 0.003 0.030 1303 Dihedral : 4.596 43.440 1017 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.74 % Allowed : 27.09 % Favored : 68.16 % 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: 0.19 (0.27), residues: 948 helix: 1.88 (0.33), residues: 257 sheet: 0.12 (0.39), residues: 180 loop : -0.80 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 504 TYR 0.011 0.001 TYR D 725 PHE 0.030 0.001 PHE D 759 TRP 0.013 0.001 TRP A 442 HIS 0.005 0.001 HIS D 209 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 7535) covalent geometry : angle 0.72495 (10246) SS BOND : bond 0.00405 ( 5) SS BOND : angle 1.22236 ( 10) hydrogen bonds : bond 0.05274 ( 296) hydrogen bonds : angle 4.71450 ( 834) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 58 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: B 93 MET cc_start: 0.8851 (tpp) cc_final: 0.8614 (tpp) REVERT: D 278 HIS cc_start: 0.8193 (OUTLIER) cc_final: 0.7825 (m170) REVERT: D 419 ASP cc_start: 0.8252 (t0) cc_final: 0.7858 (t0) REVERT: D 543 LEU cc_start: 0.9156 (mt) cc_final: 0.8754 (pp) REVERT: D 546 TRP cc_start: 0.7360 (OUTLIER) cc_final: 0.6915 (m-10) REVERT: D 584 ASN cc_start: 0.8501 (m110) cc_final: 0.8141 (m-40) REVERT: A 498 MET cc_start: 0.9194 (tpp) cc_final: 0.8780 (tpp) outliers start: 37 outliers final: 34 residues processed: 89 average time/residue: 0.0558 time to fit residues: 7.8115 Evaluate side-chains 92 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 56 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 546 TRP Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 725 TYR Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 778 SER Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 803 PHE Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 52 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 89 optimal weight: 0.0270 chunk 34 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 293 HIS ** D 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 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 = 0.3275 r_free = 0.3275 target = 0.069879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.049321 restraints weight = 36573.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.051229 restraints weight = 19404.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.052583 restraints weight = 12788.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.053426 restraints weight = 9532.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.054152 restraints weight = 7814.421| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7540 Z= 0.120 Angle : 0.709 12.724 10256 Z= 0.327 Chirality : 0.043 0.168 1184 Planarity : 0.003 0.029 1303 Dihedral : 4.413 42.777 1017 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.37 % Allowed : 27.59 % Favored : 68.04 % 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: 0.29 (0.28), residues: 948 helix: 1.90 (0.33), residues: 259 sheet: 0.17 (0.39), residues: 180 loop : -0.70 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 504 TYR 0.010 0.001 TYR D 725 PHE 0.029 0.001 PHE D 759 TRP 0.011 0.001 TRP A 442 HIS 0.007 0.001 HIS D 293 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7535) covalent geometry : angle 0.70852 (10246) SS BOND : bond 0.00295 ( 5) SS BOND : angle 1.14482 ( 10) hydrogen bonds : bond 0.04750 ( 296) hydrogen bonds : angle 4.59370 ( 834) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1455.44 seconds wall clock time: 25 minutes 51.09 seconds (1551.09 seconds total)