Starting phenix.real_space_refine on Tue Aug 4 19:06:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cal_45395/08_2026/9cal_45395_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cal_45395/08_2026/9cal_45395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cal_45395/08_2026/9cal_45395_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cal_45395/08_2026/9cal_45395_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cal_45395/08_2026/9cal_45395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cal_45395/08_2026/9cal_45395.map" } resolution = 3.15 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= 0.001 sd= 0.020 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 10 5.49 5 S 39 5.16 5 C 3928 2.51 5 N 1084 2.21 5 O 1206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6268 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4845 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 30, 'TRANS': 581} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1219 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "D" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 146 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "E" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Classifications: {'DNA': 3} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.42, per 1000 atoms: 0.23 Number of scatterers: 6268 At special positions: 0 Unit cell: (72.16, 86.1, 137.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 39 16.00 P 10 15.00 O 1206 8.00 N 1084 7.00 C 3928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 309.6 milliseconds 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1442 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 42.8% alpha, 14.7% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 77 through 82 removed outlier: 3.997A pdb=" N PHE A 82 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 119 through 134 Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 156 through 166 Processing helix chain 'A' and resid 171 through 201 removed outlier: 3.743A pdb=" N ALA A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.725A pdb=" N CYS A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.523A pdb=" N THR A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'A' and resid 349 through 357 removed outlier: 4.146A pdb=" N GLN A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 373 Processing helix chain 'A' and resid 404 through 421 removed outlier: 3.730A pdb=" N LEU A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 495 through 507 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 538 through 552 Processing helix chain 'A' and resid 553 through 556 Processing helix chain 'A' and resid 559 through 573 removed outlier: 3.923A pdb=" N LEU A 570 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE A 571 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 599 Processing helix chain 'A' and resid 600 through 611 removed outlier: 3.742A pdb=" N LEU A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 17 through 25 removed outlier: 3.505A pdb=" N THR B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 41 Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 56 through 60 removed outlier: 4.256A pdb=" N GLY B 60 " --> pdb=" O ILE B 57 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 6.557A pdb=" N LYS A 2 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LYS A 53 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL A 4 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR A 3 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL A 113 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU A 5 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE A 112 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 66 Processing sheet with id=AA3, first strand: chain 'A' and resid 254 through 256 removed outlier: 6.569A pdb=" N VAL A 242 " --> pdb=" O MET A 483 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N MET A 483 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLN A 244 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL A 481 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS A 246 " --> pdb=" O GLY A 479 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 259 removed outlier: 7.258A pdb=" N LYS A 425 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 426 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 430 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA A 287 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG A 434 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL A 285 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA6, first strand: chain 'B' and resid 135 through 136 removed outlier: 9.347A pdb=" N LEU B 140 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR B 107 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU B 142 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL B 109 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU B 95 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG B 96 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE B 76 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLN B 98 " --> pdb=" O GLN B 74 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS B 69 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LYS B 126 " --> pdb=" O LEU B 150 " (cutoff:3.500A) 267 hydrogen bonds defined for protein. 756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 0.88 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: 1.22 - 1.34: 1966 1.34 - 1.45: 875 1.45 - 1.57: 3495 1.57 - 1.69: 18 1.69 - 1.81: 61 Bond restraints: 6415 Sorted by residual: bond pdb=" OH PTR A 336 " pdb=" P PTR A 336 " ideal model delta sigma weight residual 1.769 1.608 0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" C SER A 335 " pdb=" N PTR A 336 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.18e+01 bond pdb=" O1P PTR A 336 " pdb=" P PTR A 336 " ideal model delta sigma weight residual 1.522 1.477 0.045 2.00e-02 2.50e+03 5.03e+00 bond pdb=" O3' DA D 3 " pdb=" P DT D 4 " ideal model delta sigma weight residual 1.607 1.583 0.024 1.20e-02 6.94e+03 4.03e+00 bond pdb=" C4' DC D 0 " pdb=" C3' DC D 0 " ideal model delta sigma weight residual 1.529 1.509 0.020 1.00e-02 1.00e+04 4.02e+00 ... (remaining 6410 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.17: 8716 6.17 - 12.34: 4 12.34 - 18.51: 1 18.51 - 24.68: 0 24.68 - 30.85: 1 Bond angle restraints: 8722 Sorted by residual: angle pdb=" O SER A 335 " pdb=" C SER A 335 " pdb=" N PTR A 336 " ideal model delta sigma weight residual 123.00 92.15 30.85 1.60e+00 3.91e-01 3.72e+02 angle pdb=" CA SER A 335 " pdb=" C SER A 335 " pdb=" N PTR A 336 " ideal model delta sigma weight residual 116.20 132.42 -16.22 2.00e+00 2.50e-01 6.58e+01 angle pdb=" N ASN A 33 " pdb=" CA ASN A 33 " pdb=" C ASN A 33 " ideal model delta sigma weight residual 114.62 109.58 5.04 1.14e+00 7.69e-01 1.95e+01 angle pdb=" C SER A 335 " pdb=" N PTR A 336 " pdb=" CA PTR A 336 " ideal model delta sigma weight residual 121.70 129.53 -7.83 1.80e+00 3.09e-01 1.89e+01 angle pdb=" N3 DT E 6 " pdb=" C4 DT E 6 " pdb=" O4 DT E 6 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 8717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3434 17.94 - 35.88: 344 35.88 - 53.81: 78 53.81 - 71.75: 9 71.75 - 89.69: 9 Dihedral angle restraints: 3874 sinusoidal: 1640 harmonic: 2234 Sorted by residual: dihedral pdb=" CA LEU A 67 " pdb=" C LEU A 67 " pdb=" N GLY A 68 " pdb=" CA GLY A 68 " ideal model delta harmonic sigma weight residual 180.00 162.78 17.22 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CG ARG A 407 " pdb=" CD ARG A 407 " pdb=" NE ARG A 407 " pdb=" CZ ARG A 407 " ideal model delta sinusoidal sigma weight residual -180.00 -135.06 -44.94 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB GLU A 238 " pdb=" CG GLU A 238 " pdb=" CD GLU A 238 " pdb=" OE1 GLU A 238 " ideal model delta sinusoidal sigma weight residual 0.00 89.69 -89.69 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 3871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 626 0.032 - 0.064: 243 0.064 - 0.096: 68 0.096 - 0.128: 35 0.128 - 0.160: 5 Chirality restraints: 977 Sorted by residual: chirality pdb=" CA PTR A 336 " pdb=" N PTR A 336 " pdb=" C PTR A 336 " pdb=" CB PTR A 336 " both_signs ideal model delta sigma weight residual False 2.35 2.51 -0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CA VAL B 31 " pdb=" N VAL B 31 " pdb=" C VAL B 31 " pdb=" CB VAL B 31 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CB VAL A 136 " pdb=" CA VAL A 136 " pdb=" CG1 VAL A 136 " pdb=" CG2 VAL A 136 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 974 not shown) Planarity restraints: 1092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 335 " 0.084 2.00e-02 2.50e+03 1.31e-01 1.73e+02 pdb=" C SER A 335 " -0.227 2.00e-02 2.50e+03 pdb=" O SER A 335 " 0.070 2.00e-02 2.50e+03 pdb=" N PTR A 336 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 476 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO A 477 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO A 477 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 477 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 436 " -0.028 5.00e-02 4.00e+02 4.38e-02 3.06e+00 pdb=" N PRO A 437 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 437 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 437 " -0.024 5.00e-02 4.00e+02 ... (remaining 1089 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 118 2.69 - 3.24: 5871 3.24 - 3.79: 9334 3.79 - 4.35: 12400 4.35 - 4.90: 20681 Nonbonded interactions: 48404 Sorted by model distance: nonbonded pdb=" OD2 ASP A 117 " pdb="MN MN A 701 " model vdw 2.136 2.320 nonbonded pdb=" OD2 ASP A 119 " pdb="MN MN A 701 " model vdw 2.173 2.320 nonbonded pdb=" OE1 GLN A 196 " pdb=" OH TYR A 548 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR A 199 " pdb=" OD2 ASP A 604 " model vdw 2.280 3.040 nonbonded pdb=" OD1 ASP A 208 " pdb=" N SER A 209 " model vdw 2.291 3.120 ... (remaining 48399 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 7.340 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 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 : 0.004 0.161 6416 Z= 0.242 Angle : 0.688 30.854 8722 Z= 0.396 Chirality : 0.041 0.160 977 Planarity : 0.006 0.131 1092 Dihedral : 15.357 89.687 2432 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.31), residues: 766 helix: 0.71 (0.30), residues: 309 sheet: -0.49 (0.49), residues: 127 loop : -0.46 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 107 TYR 0.010 0.001 TYR A 240 PHE 0.009 0.001 PHE A 101 TRP 0.020 0.002 TRP A 115 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.24 ( 6415) covalent geometry : angle 0.68804 / 0.40 ( 8722) hydrogen bonds : bond 0.19405 / 13.02 ( 267) hydrogen bonds : angle 5.61181 / 4.01 ( 756) Misc. bond : bond 0.03671 / 1.93 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 48 GLN cc_start: 0.8058 (mm110) cc_final: 0.7738 (tp40) REVERT: A 246 LYS cc_start: 0.8427 (mttm) cc_final: 0.8205 (mttp) REVERT: A 284 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7284 (mm-40) REVERT: A 425 LYS cc_start: 0.8167 (mttm) cc_final: 0.7936 (mttm) REVERT: A 434 ARG cc_start: 0.7901 (ttm170) cc_final: 0.7699 (ttm-80) REVERT: A 599 SER cc_start: 0.7750 (t) cc_final: 0.7524 (t) REVERT: B 132 ILE cc_start: 0.8604 (mm) cc_final: 0.8373 (mm) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.0715 time to fit residues: 15.3486 Evaluate side-chains 161 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.0870 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN A 218 GLN B 156 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.098680 restraints weight = 9703.491| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.03 r_work: 0.3140 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6416 Z= 0.144 Angle : 0.542 7.887 8722 Z= 0.289 Chirality : 0.041 0.215 977 Planarity : 0.004 0.068 1092 Dihedral : 11.226 87.630 946 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.05 % Allowed : 7.65 % Favored : 91.30 % 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 are not related in a simple way. whole: 0.39 (0.31), residues: 766 helix: 1.35 (0.30), residues: 306 sheet: -0.44 (0.49), residues: 125 loop : -0.40 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 107 TYR 0.011 0.001 TYR A 41 PHE 0.009 0.001 PHE A 433 TRP 0.007 0.001 TRP A 458 HIS 0.003 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 6415) covalent geometry : angle 0.54219 / 0.29 ( 8722) hydrogen bonds : bond 0.05107 / 3.49 ( 267) hydrogen bonds : angle 4.31422 / 2.98 ( 756) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 164 time to evaluate : 0.183 Fit side-chains REVERT: A 162 ASN cc_start: 0.7768 (m-40) cc_final: 0.7344 (m-40) REVERT: A 340 GLU cc_start: 0.7441 (mm-30) cc_final: 0.6977 (mm-30) REVERT: A 425 LYS cc_start: 0.8464 (mttm) cc_final: 0.8260 (mttp) REVERT: A 434 ARG cc_start: 0.8397 (ttm170) cc_final: 0.8111 (ttm-80) REVERT: A 587 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7865 (m-30) REVERT: A 599 SER cc_start: 0.8308 (t) cc_final: 0.8058 (t) REVERT: B 132 ILE cc_start: 0.8664 (mm) cc_final: 0.8402 (mm) outliers start: 7 outliers final: 4 residues processed: 164 average time/residue: 0.0722 time to fit residues: 15.2005 Evaluate side-chains 165 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 160 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 21 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.098139 restraints weight = 9700.765| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.02 r_work: 0.3131 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6416 Z= 0.171 Angle : 0.525 5.486 8722 Z= 0.281 Chirality : 0.042 0.196 977 Planarity : 0.004 0.057 1092 Dihedral : 11.194 88.001 946 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.95 % Allowed : 9.60 % Favored : 88.46 % 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 are not related in a simple way. whole: 0.50 (0.31), residues: 766 helix: 1.56 (0.30), residues: 305 sheet: -0.39 (0.48), residues: 127 loop : -0.46 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 107 TYR 0.015 0.002 TYR A 578 PHE 0.011 0.001 PHE A 101 TRP 0.007 0.001 TRP A 458 HIS 0.004 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 6415) covalent geometry : angle 0.52507 / 0.28 ( 8722) hydrogen bonds : bond 0.04756 / 3.24 ( 267) hydrogen bonds : angle 4.09717 / 2.84 ( 756) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.130 Fit side-chains REVERT: A 587 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7839 (m-30) REVERT: A 598 ASP cc_start: 0.8331 (m-30) cc_final: 0.7219 (t0) REVERT: A 599 SER cc_start: 0.8299 (t) cc_final: 0.8028 (t) REVERT: B 132 ILE cc_start: 0.8670 (mm) cc_final: 0.8419 (mm) outliers start: 13 outliers final: 7 residues processed: 165 average time/residue: 0.0676 time to fit residues: 14.2748 Evaluate side-chains 170 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 51 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 50 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.0570 chunk 24 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.109709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.098618 restraints weight = 9680.942| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.03 r_work: 0.3138 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6416 Z= 0.143 Angle : 0.512 5.941 8722 Z= 0.273 Chirality : 0.041 0.193 977 Planarity : 0.004 0.051 1092 Dihedral : 11.142 89.249 946 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.10 % Allowed : 13.04 % Favored : 84.86 % 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 are not related in a simple way. whole: 0.56 (0.31), residues: 766 helix: 1.65 (0.30), residues: 304 sheet: -0.41 (0.46), residues: 140 loop : -0.43 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 107 TYR 0.015 0.001 TYR A 578 PHE 0.009 0.001 PHE A 433 TRP 0.007 0.001 TRP A 458 HIS 0.003 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 6415) covalent geometry : angle 0.51161 / 0.27 ( 8722) hydrogen bonds : bond 0.04339 / 2.94 ( 267) hydrogen bonds : angle 4.04578 / 2.83 ( 756) Misc. bond : bond 0.00030 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.164 Fit side-chains REVERT: A 423 ASP cc_start: 0.8299 (m-30) cc_final: 0.7928 (m-30) REVERT: A 504 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7183 (tm-30) REVERT: A 587 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7807 (m-30) REVERT: A 598 ASP cc_start: 0.8321 (m-30) cc_final: 0.7199 (t0) REVERT: A 599 SER cc_start: 0.8289 (t) cc_final: 0.8005 (t) REVERT: B 132 ILE cc_start: 0.8673 (mm) cc_final: 0.8425 (mm) outliers start: 14 outliers final: 11 residues processed: 161 average time/residue: 0.0717 time to fit residues: 14.8012 Evaluate side-chains 170 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 51 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 33 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 59 optimal weight: 0.1980 chunk 7 optimal weight: 0.0770 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 32 optimal weight: 0.3980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.109609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.098450 restraints weight = 9821.384| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.06 r_work: 0.3135 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6416 Z= 0.142 Angle : 0.502 4.796 8722 Z= 0.269 Chirality : 0.041 0.187 977 Planarity : 0.004 0.048 1092 Dihedral : 11.088 86.351 946 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.55 % Allowed : 14.24 % Favored : 83.21 % 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 are not related in a simple way. whole: 0.60 (0.31), residues: 766 helix: 1.67 (0.31), residues: 303 sheet: -0.38 (0.46), residues: 140 loop : -0.39 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 107 TYR 0.015 0.001 TYR A 578 PHE 0.009 0.001 PHE A 127 TRP 0.007 0.001 TRP A 458 HIS 0.004 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 6415) covalent geometry : angle 0.50195 / 0.27 ( 8722) hydrogen bonds : bond 0.04185 / 2.82 ( 267) hydrogen bonds : angle 3.96234 / 2.78 ( 756) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.162 Fit side-chains REVERT: A 33 ASN cc_start: 0.8079 (m-40) cc_final: 0.7750 (t0) REVERT: A 423 ASP cc_start: 0.8301 (m-30) cc_final: 0.7919 (m-30) REVERT: A 504 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7183 (tm-30) REVERT: A 587 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7801 (m-30) REVERT: A 598 ASP cc_start: 0.8271 (m-30) cc_final: 0.7199 (t0) REVERT: A 599 SER cc_start: 0.8273 (t) cc_final: 0.7984 (t) REVERT: A 606 LEU cc_start: 0.8187 (mt) cc_final: 0.7877 (mp) REVERT: B 132 ILE cc_start: 0.8685 (mm) cc_final: 0.8448 (mm) outliers start: 17 outliers final: 11 residues processed: 166 average time/residue: 0.0763 time to fit residues: 16.0019 Evaluate side-chains 172 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 51 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 chunk 56 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.098040 restraints weight = 9731.367| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.03 r_work: 0.3132 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6416 Z= 0.167 Angle : 0.514 4.834 8722 Z= 0.275 Chirality : 0.041 0.180 977 Planarity : 0.004 0.046 1092 Dihedral : 11.049 83.146 946 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.10 % Allowed : 14.84 % Favored : 83.06 % 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 are not related in a simple way. whole: 0.61 (0.31), residues: 766 helix: 1.69 (0.31), residues: 302 sheet: -0.34 (0.46), residues: 140 loop : -0.41 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 107 TYR 0.016 0.001 TYR A 578 PHE 0.010 0.001 PHE A 127 TRP 0.007 0.001 TRP A 458 HIS 0.004 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 6415) covalent geometry : angle 0.51404 / 0.28 ( 8722) hydrogen bonds : bond 0.04375 / 2.95 ( 267) hydrogen bonds : angle 4.02483 / 2.84 ( 756) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.213 Fit side-chains REVERT: A 15 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7608 (tt0) REVERT: A 48 GLN cc_start: 0.8217 (mm110) cc_final: 0.8004 (tp40) REVERT: A 423 ASP cc_start: 0.8333 (m-30) cc_final: 0.7931 (m-30) REVERT: A 504 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7173 (tm-30) REVERT: A 587 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: A 598 ASP cc_start: 0.8274 (m-30) cc_final: 0.7216 (t0) REVERT: A 599 SER cc_start: 0.8268 (t) cc_final: 0.7965 (t) REVERT: A 606 LEU cc_start: 0.8186 (mt) cc_final: 0.7877 (mp) REVERT: B 132 ILE cc_start: 0.8692 (mm) cc_final: 0.8448 (mm) outliers start: 14 outliers final: 11 residues processed: 164 average time/residue: 0.0749 time to fit residues: 15.6168 Evaluate side-chains 174 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 51 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 33 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 35 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.097548 restraints weight = 9784.970| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.05 r_work: 0.3124 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6416 Z= 0.184 Angle : 0.529 7.138 8722 Z= 0.281 Chirality : 0.042 0.178 977 Planarity : 0.004 0.046 1092 Dihedral : 10.991 79.063 946 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.40 % Allowed : 15.44 % Favored : 82.16 % 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 are not related in a simple way. whole: 0.59 (0.31), residues: 766 helix: 1.67 (0.31), residues: 301 sheet: -0.34 (0.46), residues: 140 loop : -0.43 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 107 TYR 0.017 0.002 TYR A 578 PHE 0.011 0.001 PHE A 127 TRP 0.007 0.001 TRP A 458 HIS 0.005 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 ( 6415) covalent geometry : angle 0.52939 / 0.28 ( 8722) hydrogen bonds : bond 0.04430 / 2.98 ( 267) hydrogen bonds : angle 3.98706 / 2.80 ( 756) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.142 Fit side-chains REVERT: A 32 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8726 (pp) REVERT: A 48 GLN cc_start: 0.8246 (mm110) cc_final: 0.8036 (tp40) REVERT: A 383 ASP cc_start: 0.7752 (t0) cc_final: 0.7526 (t0) REVERT: A 423 ASP cc_start: 0.8335 (m-30) cc_final: 0.7884 (m-30) REVERT: A 504 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7199 (tm-30) REVERT: A 587 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: A 598 ASP cc_start: 0.8289 (m-30) cc_final: 0.7243 (t0) REVERT: A 599 SER cc_start: 0.8312 (t) cc_final: 0.7998 (t) REVERT: A 606 LEU cc_start: 0.8220 (mt) cc_final: 0.7904 (mp) REVERT: B 132 ILE cc_start: 0.8700 (mm) cc_final: 0.8464 (mm) outliers start: 16 outliers final: 12 residues processed: 171 average time/residue: 0.0774 time to fit residues: 16.6888 Evaluate side-chains 178 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 51 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 49 optimal weight: 0.0050 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 0.0470 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.2692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.110175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.099095 restraints weight = 9762.563| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.04 r_work: 0.3151 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6416 Z= 0.114 Angle : 0.505 7.575 8722 Z= 0.268 Chirality : 0.040 0.174 977 Planarity : 0.005 0.087 1092 Dihedral : 10.956 76.808 946 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.10 % Allowed : 16.19 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.31), residues: 766 helix: 1.63 (0.31), residues: 303 sheet: -0.38 (0.45), residues: 140 loop : -0.34 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 107 TYR 0.014 0.001 TYR A 578 PHE 0.010 0.001 PHE A 433 TRP 0.007 0.001 TRP A 241 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 6415) covalent geometry : angle 0.50532 / 0.27 ( 8722) hydrogen bonds : bond 0.04005 / 2.67 ( 267) hydrogen bonds : angle 3.98286 / 2.81 ( 756) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.246 Fit side-chains REVERT: A 15 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7584 (tt0) REVERT: A 504 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7157 (tm-30) REVERT: A 599 SER cc_start: 0.8257 (t) cc_final: 0.7901 (t) REVERT: A 606 LEU cc_start: 0.8175 (mt) cc_final: 0.7854 (mp) outliers start: 14 outliers final: 9 residues processed: 163 average time/residue: 0.0782 time to fit residues: 16.1938 Evaluate side-chains 164 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 51 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 45 optimal weight: 0.0000 chunk 48 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 6 optimal weight: 0.0870 chunk 7 optimal weight: 0.0470 chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.3660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.109994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.098849 restraints weight = 9834.537| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.04 r_work: 0.3149 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6416 Z= 0.131 Angle : 0.522 8.017 8722 Z= 0.274 Chirality : 0.040 0.170 977 Planarity : 0.005 0.079 1092 Dihedral : 10.919 75.371 946 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.80 % Allowed : 17.69 % Favored : 80.51 % 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 are not related in a simple way. whole: 0.67 (0.31), residues: 766 helix: 1.64 (0.31), residues: 303 sheet: -0.30 (0.46), residues: 138 loop : -0.28 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 107 TYR 0.015 0.001 TYR A 578 PHE 0.010 0.001 PHE A 433 TRP 0.006 0.001 TRP A 241 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 6415) covalent geometry : angle 0.52198 / 0.27 ( 8722) hydrogen bonds : bond 0.04010 / 2.67 ( 267) hydrogen bonds : angle 3.92041 / 2.75 ( 756) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.135 Fit side-chains REVERT: A 15 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7596 (tt0) REVERT: A 32 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8608 (pp) REVERT: A 427 LEU cc_start: 0.8616 (tt) cc_final: 0.8387 (tp) REVERT: A 504 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7148 (tm-30) REVERT: A 599 SER cc_start: 0.8268 (t) cc_final: 0.7913 (t) REVERT: A 606 LEU cc_start: 0.8150 (mt) cc_final: 0.7822 (mp) outliers start: 12 outliers final: 8 residues processed: 160 average time/residue: 0.0762 time to fit residues: 15.4718 Evaluate side-chains 165 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 51 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 39 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 6 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.109283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.098172 restraints weight = 9650.798| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.01 r_work: 0.3142 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6416 Z= 0.160 Angle : 0.531 7.965 8722 Z= 0.281 Chirality : 0.041 0.164 977 Planarity : 0.005 0.078 1092 Dihedral : 10.892 73.519 946 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.65 % Allowed : 17.09 % Favored : 81.26 % 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 are not related in a simple way. whole: 0.66 (0.31), residues: 766 helix: 1.63 (0.31), residues: 304 sheet: -0.19 (0.46), residues: 140 loop : -0.35 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 107 TYR 0.017 0.001 TYR A 578 PHE 0.010 0.001 PHE A 127 TRP 0.006 0.001 TRP A 458 HIS 0.004 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 6415) covalent geometry : angle 0.53106 / 0.28 ( 8722) hydrogen bonds : bond 0.04214 / 2.82 ( 267) hydrogen bonds : angle 3.93441 / 2.76 ( 756) Misc. bond : bond 0.00015 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.128 Fit side-chains REVERT: A 15 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7609 (tt0) REVERT: A 48 GLN cc_start: 0.8237 (mm110) cc_final: 0.8028 (tp40) REVERT: A 427 LEU cc_start: 0.8625 (tt) cc_final: 0.8399 (tp) REVERT: A 504 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7147 (tm-30) REVERT: A 599 SER cc_start: 0.8268 (t) cc_final: 0.7913 (t) REVERT: A 606 LEU cc_start: 0.8154 (mt) cc_final: 0.7843 (mp) outliers start: 11 outliers final: 10 residues processed: 156 average time/residue: 0.0808 time to fit residues: 15.8709 Evaluate side-chains 163 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 51 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 75 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.0370 chunk 18 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 21 optimal weight: 0.0670 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.098555 restraints weight = 9724.044| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.03 r_work: 0.3144 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6416 Z= 0.142 Angle : 0.529 7.943 8722 Z= 0.279 Chirality : 0.041 0.164 977 Planarity : 0.004 0.075 1092 Dihedral : 10.862 71.755 946 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.80 % Allowed : 17.39 % Favored : 80.81 % 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 are not related in a simple way. whole: 0.65 (0.31), residues: 766 helix: 1.60 (0.31), residues: 304 sheet: -0.17 (0.46), residues: 140 loop : -0.33 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 107 TYR 0.016 0.001 TYR A 578 PHE 0.012 0.001 PHE A 433 TRP 0.006 0.001 TRP A 458 HIS 0.003 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 6415) covalent geometry : angle 0.52857 / 0.28 ( 8722) hydrogen bonds : bond 0.04051 / 2.70 ( 267) hydrogen bonds : angle 3.90956 / 2.75 ( 756) Misc. bond : bond 0.00005 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1384.84 seconds wall clock time: 24 minutes 22.95 seconds (1462.95 seconds total)