Starting phenix.real_space_refine on Thu Jul 2 03:14:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cal_45395/07_2026/9cal_45395_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cal_45395/07_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_45395/07_2026/9cal_45395_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cal_45395/07_2026/9cal_45395_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cal_45395/07_2026/9cal_45395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cal_45395/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Time building chain proxies: 1.63, per 1000 atoms: 0.26 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: 0.47 Conformation dependent library (CDL) restraints added in 414.0 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: 0.68 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: 1.08 Time building geometry restraints manager: 0.66 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=" 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 bond pdb=" CZ PTR A 336 " pdb=" OH PTR A 336 " ideal model delta sigma weight residual 1.339 1.300 0.039 2.00e-02 2.50e+03 3.84e+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 3.060 nonbonded pdb=" OD2 ASP A 119 " pdb="MN MN A 701 " model vdw 2.173 3.060 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: 4.000 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.400 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: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.560 ------------------------------------------------------------------------------- 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= 0.241 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 0.68791 / 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 : 0.221 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: 0.0915 time to fit residues: 19.6090 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 : 0.272 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.109712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098648 restraints weight = 9716.044| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.03 r_work: 0.3141 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.0828 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 7.739 8722 Z= 0.289 Chirality : 0.041 0.216 977 Planarity : 0.004 0.068 1092 Dihedral : 11.231 87.354 946 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % 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 0.012 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 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 6415) covalent geometry : angle 0.54223 / 0.29 ( 8722) hydrogen bonds : bond 0.05076 / 3.46 ( 267) hydrogen bonds : angle 4.30482 / 2.97 ( 756) Misc. bond : bond 0.00106 / 0.06 ( 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 : 0.229 Fit side-chains REVERT: A 162 ASN cc_start: 0.7772 (m-40) cc_final: 0.7348 (m-40) REVERT: A 340 GLU cc_start: 0.7452 (mm-30) cc_final: 0.6988 (mm-30) REVERT: A 425 LYS cc_start: 0.8465 (mttm) cc_final: 0.8262 (mttp) REVERT: A 434 ARG cc_start: 0.8398 (ttm170) cc_final: 0.8111 (ttm-80) REVERT: A 587 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7859 (m-30) REVERT: A 599 SER cc_start: 0.8309 (t) cc_final: 0.8060 (t) REVERT: B 132 ILE cc_start: 0.8664 (mm) cc_final: 0.8403 (mm) outliers start: 7 outliers final: 4 residues processed: 164 average time/residue: 0.0902 time to fit residues: 18.8208 Evaluate side-chains 166 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 161 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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: 0.7980 chunk 6 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 38 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 13 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.109750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.098749 restraints weight = 9689.493| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.02 r_work: 0.3139 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: 0.8267 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6416 Z= 0.148 Angle : 0.513 5.577 8722 Z= 0.275 Chirality : 0.041 0.193 977 Planarity : 0.004 0.056 1092 Dihedral : 11.192 87.948 946 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.95 % Allowed : 9.30 % Favored : 88.76 % 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: 0.52 (0.31), residues: 766 helix: 1.57 (0.30), residues: 305 sheet: -0.38 (0.48), residues: 127 loop : -0.44 (0.34), residues: 334 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 0.011 0.001 PHE A 433 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 0.00333 / 0.15 ( 6415) covalent geometry : angle 0.51326 / 0.27 ( 8722) hydrogen bonds : bond 0.04607 / 3.14 ( 267) hydrogen bonds : angle 4.08967 / 2.84 ( 756) Misc. bond : bond 0.00001 / 0.00 ( 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 175 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.231 Fit side-chains REVERT: A 423 ASP cc_start: 0.8292 (m-30) cc_final: 0.7946 (m-30) REVERT: A 587 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7827 (m-30) REVERT: A 598 ASP cc_start: 0.8329 (m-30) cc_final: 0.7217 (t0) REVERT: A 599 SER cc_start: 0.8283 (t) cc_final: 0.8025 (t) REVERT: B 132 ILE cc_start: 0.8667 (mm) cc_final: 0.8420 (mm) outliers start: 13 outliers final: 7 residues processed: 163 average time/residue: 0.0834 time to fit residues: 17.4497 Evaluate side-chains 169 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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 587 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 21 ILE 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: 0.8980 chunk 52 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.109401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.098348 restraints weight = 9714.539| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.03 r_work: 0.3133 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6416 Z= 0.160 Angle : 0.519 6.229 8722 Z= 0.276 Chirality : 0.041 0.191 977 Planarity : 0.004 0.051 1092 Dihedral : 11.152 89.368 946 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.10 % Allowed : 12.59 % Favored : 85.31 % 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: 1.62 (0.30), residues: 305 sheet: -0.38 (0.46), residues: 142 loop : -0.42 (0.35), residues: 319 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 0.004 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 6415) covalent geometry : angle 0.51917 / 0.28 ( 8722) hydrogen bonds : bond 0.04464 / 3.02 ( 267) hydrogen bonds : angle 4.06481 / 2.84 ( 756) Misc. bond : bond 0.00029 / 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 : 0.210 Fit side-chains REVERT: A 504 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7176 (tm-30) REVERT: A 587 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7822 (m-30) REVERT: A 598 ASP cc_start: 0.8324 (m-30) cc_final: 0.7243 (t0) REVERT: A 599 SER cc_start: 0.8295 (t) cc_final: 0.8015 (t) REVERT: B 132 ILE cc_start: 0.8675 (mm) cc_final: 0.8428 (mm) outliers start: 14 outliers final: 11 residues processed: 162 average time/residue: 0.0814 time to fit residues: 16.9739 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 : 0.185 ------------------------------------------------------------------------------- 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 373 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=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: 0.8980 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 6 optimal weight: 0.4980 chunk 32 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 = 0.3409 r_free = 0.3409 target = 0.109297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.098206 restraints weight = 9834.205| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.05 r_work: 0.3130 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6416 Z= 0.167 Angle : 0.514 4.827 8722 Z= 0.275 Chirality : 0.041 0.189 977 Planarity : 0.004 0.049 1092 Dihedral : 11.105 86.150 946 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.25 % Allowed : 14.09 % Favored : 83.66 % 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: 1.69 (0.31), residues: 302 sheet: -0.40 (0.46), residues: 140 loop : -0.43 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 107 TYR 0.016 0.002 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 0.00390 / 0.17 ( 6415) covalent geometry : angle 0.51376 / 0.27 ( 8722) hydrogen bonds : bond 0.04394 / 2.98 ( 267) hydrogen bonds : angle 3.99657 / 2.80 ( 756) Misc. bond : bond 0.00026 / 0.01 ( 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 178 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.137 Fit side-chains REVERT: A 423 ASP cc_start: 0.8296 (m-30) cc_final: 0.7931 (m-30) REVERT: A 504 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7172 (tm-30) REVERT: A 587 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7804 (m-30) REVERT: A 598 ASP cc_start: 0.8323 (m-30) cc_final: 0.7271 (t0) REVERT: A 599 SER cc_start: 0.8314 (t) cc_final: 0.8019 (t) REVERT: A 606 LEU cc_start: 0.8197 (mt) cc_final: 0.7872 (mp) REVERT: B 132 ILE cc_start: 0.8682 (mm) cc_final: 0.8441 (mm) outliers start: 15 outliers final: 10 residues processed: 165 average time/residue: 0.0818 time to fit residues: 17.2256 Evaluate side-chains 171 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 340 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 56 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.109085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.098041 restraints weight = 9753.497| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.03 r_work: 0.3131 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6416 Z= 0.172 Angle : 0.517 4.831 8722 Z= 0.278 Chirality : 0.041 0.183 977 Planarity : 0.004 0.047 1092 Dihedral : 11.071 83.236 946 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.70 % Allowed : 14.24 % 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: 0.59 (0.31), residues: 766 helix: 1.67 (0.31), residues: 302 sheet: -0.34 (0.47), residues: 140 loop : -0.43 (0.34), residues: 324 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 0.009 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 0.00403 / 0.17 ( 6415) covalent geometry : angle 0.51669 / 0.28 ( 8722) hydrogen bonds : bond 0.04415 / 2.97 ( 267) hydrogen bonds : angle 4.03173 / 2.84 ( 756) Misc. bond : bond 0.00029 / 0.02 ( 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 182 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.285 Fit side-chains REVERT: A 48 GLN cc_start: 0.8232 (mm110) cc_final: 0.8018 (tp40) REVERT: A 383 ASP cc_start: 0.7730 (t0) cc_final: 0.7503 (t0) REVERT: A 423 ASP cc_start: 0.8306 (m-30) cc_final: 0.7923 (m-30) REVERT: A 504 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7164 (tm-30) REVERT: A 587 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7809 (m-30) REVERT: A 598 ASP cc_start: 0.8298 (m-30) cc_final: 0.7245 (t0) REVERT: A 599 SER cc_start: 0.8268 (t) cc_final: 0.7960 (t) REVERT: A 606 LEU cc_start: 0.8187 (mt) cc_final: 0.7873 (mp) REVERT: B 132 ILE cc_start: 0.8693 (mm) cc_final: 0.8444 (mm) outliers start: 18 outliers final: 13 residues processed: 168 average time/residue: 0.0834 time to fit residues: 17.8386 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 : 0.137 ------------------------------------------------------------------------------- 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 136 VAL 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 327 ARG Chi-restraints excluded: chain A residue 373 GLU 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 Chi-restraints excluded: chain B residue 114 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 0.0070 chunk 43 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 39 optimal weight: 0.0970 chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.109564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098562 restraints weight = 9740.600| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.04 r_work: 0.3141 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6416 Z= 0.129 Angle : 0.500 4.952 8722 Z= 0.267 Chirality : 0.040 0.174 977 Planarity : 0.004 0.044 1092 Dihedral : 11.017 80.670 946 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.10 % Allowed : 16.04 % Favored : 81.86 % 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: 0.62 (0.31), residues: 766 helix: 1.69 (0.31), residues: 303 sheet: -0.39 (0.46), residues: 140 loop : -0.36 (0.35), residues: 323 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 0.009 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 0.00296 / 0.13 ( 6415) covalent geometry : angle 0.50041 / 0.27 ( 8722) hydrogen bonds : bond 0.04086 / 2.74 ( 267) hydrogen bonds : angle 3.95257 / 2.78 ( 756) Misc. bond : bond 0.00012 / 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 176 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.239 Fit side-chains REVERT: A 145 LYS cc_start: 0.8812 (mtpt) cc_final: 0.8587 (mtpp) REVERT: A 423 ASP cc_start: 0.8301 (m-30) cc_final: 0.7910 (m-30) REVERT: A 504 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7168 (tm-30) REVERT: A 587 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7807 (m-30) REVERT: A 598 ASP cc_start: 0.8258 (m-30) cc_final: 0.7212 (t0) REVERT: A 599 SER cc_start: 0.8237 (t) cc_final: 0.7915 (t) REVERT: A 606 LEU cc_start: 0.8200 (mt) cc_final: 0.7888 (mp) REVERT: B 132 ILE cc_start: 0.8709 (mm) cc_final: 0.8465 (mm) outliers start: 14 outliers final: 11 residues processed: 165 average time/residue: 0.0906 time to fit residues: 18.9083 Evaluate side-chains 168 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 136 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 198 LYS 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 Chi-restraints excluded: chain B residue 114 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 30 optimal weight: 0.6980 chunk 43 optimal weight: 0.0970 chunk 66 optimal weight: 0.8980 chunk 7 optimal weight: 0.0670 chunk 49 optimal weight: 0.0000 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 overall best weight: 0.2320 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.110443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.099452 restraints weight = 9764.178| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.04 r_work: 0.3154 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6416 Z= 0.108 Angle : 0.506 7.602 8722 Z= 0.264 Chirality : 0.040 0.172 977 Planarity : 0.004 0.046 1092 Dihedral : 10.971 78.650 946 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % 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: 0.70 (0.31), residues: 766 helix: 1.74 (0.31), residues: 303 sheet: -0.37 (0.46), residues: 138 loop : -0.30 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 107 TYR 0.013 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 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 6415) covalent geometry : angle 0.50553 / 0.26 ( 8722) hydrogen bonds : bond 0.03812 / 2.55 ( 267) hydrogen bonds : angle 3.84176 / 2.70 ( 756) Misc. bond : bond 0.00019 / 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 176 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.184 Fit side-chains REVERT: A 145 LYS cc_start: 0.8767 (mtpt) cc_final: 0.8512 (mtpp) REVERT: A 423 ASP cc_start: 0.8293 (m-30) cc_final: 0.7892 (m-30) REVERT: A 427 LEU cc_start: 0.8619 (tt) cc_final: 0.8385 (tp) REVERT: A 504 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7138 (tm-30) REVERT: A 598 ASP cc_start: 0.8231 (m-30) cc_final: 0.7500 (m-30) REVERT: A 599 SER cc_start: 0.8224 (t) cc_final: 0.7873 (t) REVERT: A 606 LEU cc_start: 0.8148 (mt) cc_final: 0.7838 (mp) outliers start: 11 outliers final: 10 residues processed: 166 average time/residue: 0.0895 time to fit residues: 18.8325 Evaluate side-chains 171 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 114 MET 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: 0.7980 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 6 optimal weight: 0.1980 chunk 7 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.109411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.098273 restraints weight = 9834.241| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.05 r_work: 0.3141 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6416 Z= 0.164 Angle : 0.542 12.230 8722 Z= 0.281 Chirality : 0.041 0.166 977 Planarity : 0.004 0.045 1092 Dihedral : 10.926 76.599 946 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.65 % Allowed : 17.39 % Favored : 80.96 % 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: 0.68 (0.31), residues: 766 helix: 1.69 (0.31), residues: 303 sheet: -0.25 (0.46), residues: 140 loop : -0.33 (0.35), residues: 323 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 0.006 0.001 TRP A 458 HIS 0.004 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 6415) covalent geometry : angle 0.54185 / 0.28 ( 8722) hydrogen bonds : bond 0.04245 / 2.85 ( 267) hydrogen bonds : angle 3.94690 / 2.79 ( 756) Misc. bond : bond 0.00022 / 0.01 ( 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 171 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.250 Fit side-chains REVERT: A 48 GLN cc_start: 0.8232 (mm110) cc_final: 0.8024 (tp40) REVERT: A 145 LYS cc_start: 0.8770 (mtpt) cc_final: 0.8525 (mtpp) REVERT: A 423 ASP cc_start: 0.8311 (m-30) cc_final: 0.7844 (m-30) REVERT: A 427 LEU cc_start: 0.8622 (tt) cc_final: 0.8392 (tp) REVERT: A 504 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7147 (tm-30) REVERT: A 598 ASP cc_start: 0.8273 (m-30) cc_final: 0.7562 (m-30) REVERT: A 599 SER cc_start: 0.8291 (t) cc_final: 0.7942 (t) REVERT: A 606 LEU cc_start: 0.8165 (mt) cc_final: 0.7835 (mp) outliers start: 11 outliers final: 9 residues processed: 162 average time/residue: 0.0822 time to fit residues: 17.0617 Evaluate side-chains 168 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 373 GLU 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 Chi-restraints excluded: chain B residue 114 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 39 optimal weight: 0.0030 chunk 68 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.0470 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 74 optimal weight: 0.0980 chunk 6 optimal weight: 0.0770 overall best weight: 0.1646 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.111546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.100331 restraints weight = 9630.275| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.04 r_work: 0.3171 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 6416 Z= 0.102 Angle : 0.517 12.022 8722 Z= 0.268 Chirality : 0.039 0.164 977 Planarity : 0.005 0.088 1092 Dihedral : 10.892 73.928 946 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.20 % Allowed : 17.69 % Favored : 81.11 % 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: 0.74 (0.31), residues: 766 helix: 1.70 (0.31), residues: 304 sheet: -0.22 (0.46), residues: 140 loop : -0.27 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 107 TYR 0.011 0.001 TYR A 578 PHE 0.006 0.001 PHE A 433 TRP 0.009 0.001 TRP A 241 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 6415) covalent geometry : angle 0.51740 / 0.27 ( 8722) hydrogen bonds : bond 0.03606 / 2.38 ( 267) hydrogen bonds : angle 3.85824 / 2.73 ( 756) Misc. bond : bond 0.00042 / 0.02 ( 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: 8 poor density : 158 time to evaluate : 0.180 Fit side-chains REVERT: A 145 LYS cc_start: 0.8751 (mtpt) cc_final: 0.8496 (mtpp) REVERT: A 427 LEU cc_start: 0.8576 (tt) cc_final: 0.8350 (tp) REVERT: A 504 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7100 (tm-30) REVERT: A 598 ASP cc_start: 0.8215 (m-30) cc_final: 0.7436 (m-30) REVERT: A 599 SER cc_start: 0.8263 (t) cc_final: 0.7896 (t) REVERT: A 606 LEU cc_start: 0.8149 (mt) cc_final: 0.7844 (mp) outliers start: 8 outliers final: 6 residues processed: 161 average time/residue: 0.0885 time to fit residues: 18.2410 Evaluate side-chains 162 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 156 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 75 optimal weight: 0.0970 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.0770 chunk 18 optimal weight: 0.8980 chunk 72 optimal weight: 0.0170 chunk 21 optimal weight: 0.4980 chunk 13 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 54 optimal weight: 0.5980 overall best weight: 0.2174 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.111242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.100016 restraints weight = 9746.614| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.05 r_work: 0.3166 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6416 Z= 0.111 Angle : 0.534 13.899 8722 Z= 0.275 Chirality : 0.039 0.156 977 Planarity : 0.004 0.079 1092 Dihedral : 10.832 72.315 946 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.90 % Allowed : 18.44 % Favored : 80.66 % 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: 0.81 (0.31), residues: 766 helix: 1.76 (0.31), residues: 304 sheet: -0.18 (0.46), residues: 140 loop : -0.25 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 107 TYR 0.012 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 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 6415) covalent geometry : angle 0.53370 / 0.28 ( 8722) hydrogen bonds : bond 0.03688 / 2.44 ( 267) hydrogen bonds : angle 3.81914 / 2.71 ( 756) Misc. bond : bond 0.00024 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1615.40 seconds wall clock time: 28 minutes 25.86 seconds (1705.86 seconds total)