Starting phenix.real_space_refine on Tue Feb 11 10:42:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lq6_23482/02_2025/7lq6_23482.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lq6_23482/02_2025/7lq6_23482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lq6_23482/02_2025/7lq6_23482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lq6_23482/02_2025/7lq6_23482.map" model { file = "/net/cci-nas-00/data/ceres_data/7lq6_23482/02_2025/7lq6_23482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lq6_23482/02_2025/7lq6_23482.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 3332 2.51 5 N 932 2.21 5 O 978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5267 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 5267 Classifications: {'peptide': 672} Link IDs: {'PTRANS': 39, 'TRANS': 632} Chain breaks: 5 Time building chain proxies: 4.30, per 1000 atoms: 0.82 Number of scatterers: 5267 At special positions: 0 Unit cell: (65.832, 86.932, 127.444, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 978 8.00 N 932 7.00 C 3332 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: 1.39 Conformation dependent library (CDL) restraints added in 638.9 milliseconds 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1250 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 41.8% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 120 through 129 removed outlier: 3.598A pdb=" N LYS A 126 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.857A pdb=" N VAL A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 277 removed outlier: 3.513A pdb=" N VAL A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 301 removed outlier: 3.614A pdb=" N ALA A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 removed outlier: 4.020A pdb=" N LEU A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 335 Processing helix chain 'A' and resid 338 through 342 removed outlier: 3.599A pdb=" N LEU A 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 removed outlier: 3.656A pdb=" N ALA A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 381 removed outlier: 3.519A pdb=" N GLU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 397 removed outlier: 3.583A pdb=" N ALA A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 397 " --> pdb=" O MET A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.083A pdb=" N LEU A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 433 removed outlier: 4.003A pdb=" N LYS A 431 " --> pdb=" O ASP A 428 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 433 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 466 removed outlier: 3.619A pdb=" N GLU A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Proline residue: A 459 - end of helix removed outlier: 4.003A pdb=" N GLN A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.911A pdb=" N LYS A 513 " --> pdb=" O SER A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'A' and resid 565 through 571 removed outlier: 4.094A pdb=" N LEU A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 571 " --> pdb=" O ASP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 585 removed outlier: 3.796A pdb=" N THR A 577 " --> pdb=" O MET A 573 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 583 " --> pdb=" O ASN A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 597 removed outlier: 4.012A pdb=" N GLU A 591 " --> pdb=" O PRO A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 617 through 630 removed outlier: 3.951A pdb=" N GLN A 623 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A 627 " --> pdb=" O GLN A 623 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 628 " --> pdb=" O ALA A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 680 removed outlier: 3.619A pdb=" N LEU A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 671 " --> pdb=" O ALA A 667 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 676 " --> pdb=" O TRP A 672 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 678 " --> pdb=" O MET A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 688 removed outlier: 3.910A pdb=" N GLY A 687 " --> pdb=" O GLY A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 705 Processing helix chain 'A' and resid 738 through 747 removed outlier: 3.533A pdb=" N ARG A 745 " --> pdb=" O SER A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 798 removed outlier: 3.974A pdb=" N GLN A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 798 " --> pdb=" O CYS A 794 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 201 through 205 removed outlier: 3.594A pdb=" N THR A 203 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA A 105 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N THR A 440 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TYR A 107 " --> pdb=" O THR A 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 113 Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 135 removed outlier: 6.144A pdb=" N ARG A 134 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL A 147 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU A 144 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 169 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A 174 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AA5, first strand: chain 'A' and resid 315 through 319 removed outlier: 3.543A pdb=" N GLY A 317 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 484 through 488 removed outlier: 6.555A pdb=" N VAL A 476 " --> pdb=" O ARG A 485 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET A 487 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE A 474 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 506 through 507 removed outlier: 3.542A pdb=" N ARG A 506 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 532 through 534 Processing sheet with id=AA9, first strand: chain 'A' and resid 633 through 634 Processing sheet with id=AB1, first strand: chain 'A' and resid 763 through 768 removed outlier: 3.597A pdb=" N ARG A 781 " --> pdb=" O VAL A 768 " (cutoff:3.500A) 188 hydrogen bonds defined for protein. 513 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1677 1.33 - 1.45: 653 1.45 - 1.57: 2988 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 5366 Sorted by residual: bond pdb=" N ARG A 337 " pdb=" CA ARG A 337 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.30e-02 5.92e+03 6.94e+00 bond pdb=" N THR A 232 " pdb=" CA THR A 232 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.22e-02 6.72e+03 6.80e+00 bond pdb=" N ASP A 234 " pdb=" CA ASP A 234 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.51e+00 bond pdb=" N GLU A 233 " pdb=" CA GLU A 233 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.08e+00 bond pdb=" N ARG A 235 " pdb=" CA ARG A 235 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.70e+00 ... (remaining 5361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 7038 1.89 - 3.78: 215 3.78 - 5.67: 12 5.67 - 7.55: 6 7.55 - 9.44: 2 Bond angle restraints: 7273 Sorted by residual: angle pdb=" O LEU A 229 " pdb=" C LEU A 229 " pdb=" N LEU A 230 " ideal model delta sigma weight residual 122.36 131.80 -9.44 1.42e+00 4.96e-01 4.42e+01 angle pdb=" CA LEU A 229 " pdb=" C LEU A 229 " pdb=" N LEU A 230 " ideal model delta sigma weight residual 117.96 109.72 8.24 1.51e+00 4.39e-01 2.98e+01 angle pdb=" N ARG A 364 " pdb=" CA ARG A 364 " pdb=" C ARG A 364 " ideal model delta sigma weight residual 112.12 105.10 7.02 1.34e+00 5.57e-01 2.74e+01 angle pdb=" N LYS A 367 " pdb=" CA LYS A 367 " pdb=" C LYS A 367 " ideal model delta sigma weight residual 114.56 107.99 6.57 1.27e+00 6.20e-01 2.67e+01 angle pdb=" N ILE A 359 " pdb=" CA ILE A 359 " pdb=" C ILE A 359 " ideal model delta sigma weight residual 111.62 107.63 3.99 7.90e-01 1.60e+00 2.55e+01 ... (remaining 7268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 2889 17.58 - 35.16: 296 35.16 - 52.74: 65 52.74 - 70.32: 18 70.32 - 87.90: 10 Dihedral angle restraints: 3278 sinusoidal: 1339 harmonic: 1939 Sorted by residual: dihedral pdb=" CA GLN A 383 " pdb=" C GLN A 383 " pdb=" N GLN A 384 " pdb=" CA GLN A 384 " ideal model delta harmonic sigma weight residual -180.00 -160.07 -19.93 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA GLN A 744 " pdb=" C GLN A 744 " pdb=" N ARG A 745 " pdb=" CA ARG A 745 " ideal model delta harmonic sigma weight residual 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASP A 762 " pdb=" CB ASP A 762 " pdb=" CG ASP A 762 " pdb=" OD1 ASP A 762 " ideal model delta sinusoidal sigma weight residual -30.00 -88.08 58.08 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 3275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 511 0.037 - 0.073: 216 0.073 - 0.110: 65 0.110 - 0.146: 24 0.146 - 0.183: 1 Chirality restraints: 817 Sorted by residual: chirality pdb=" CA ARG A 364 " pdb=" N ARG A 364 " pdb=" C ARG A 364 " pdb=" CB ARG A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CG LEU A 695 " pdb=" CB LEU A 695 " pdb=" CD1 LEU A 695 " pdb=" CD2 LEU A 695 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA LEU A 229 " pdb=" N LEU A 229 " pdb=" C LEU A 229 " pdb=" CB LEU A 229 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 814 not shown) Planarity restraints: 950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 233 " 0.013 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C GLU A 233 " -0.047 2.00e-02 2.50e+03 pdb=" O GLU A 233 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP A 234 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 586 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO A 587 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 587 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 587 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 606 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO A 607 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 607 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 607 " 0.025 5.00e-02 4.00e+02 ... (remaining 947 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 33 2.57 - 3.15: 4084 3.15 - 3.73: 7457 3.73 - 4.32: 11126 4.32 - 4.90: 18636 Nonbonded interactions: 41336 Sorted by model distance: nonbonded pdb=" CG ARG A 235 " pdb=" CB LEU A 268 " model vdw 1.987 3.840 nonbonded pdb=" O ARG A 235 " pdb=" NH1 ARG A 235 " model vdw 2.079 3.120 nonbonded pdb=" NH2 ARG A 373 " pdb=" O ARG A 397 " model vdw 2.275 3.120 nonbonded pdb=" NH1 ARG A 506 " pdb=" OD1 ASP A 707 " model vdw 2.311 3.120 nonbonded pdb=" O THR A 232 " pdb=" OG1 THR A 232 " model vdw 2.326 3.040 ... (remaining 41331 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.950 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.880 Find NCS groups from input model: 0.050 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 : 0.005 0.039 5366 Z= 0.336 Angle : 0.761 9.443 7273 Z= 0.475 Chirality : 0.045 0.183 817 Planarity : 0.005 0.050 950 Dihedral : 15.770 87.903 2028 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.45 % Favored : 94.39 % Rotamer: Outliers : 1.41 % Allowed : 3.53 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.83 (0.25), residues: 660 helix: -4.29 (0.17), residues: 252 sheet: -1.92 (0.48), residues: 100 loop : -2.55 (0.30), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 709 HIS 0.003 0.001 HIS A 179 PHE 0.016 0.002 PHE A 194 TYR 0.006 0.001 TYR A 734 ARG 0.002 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 293 MET cc_start: 0.8632 (mmt) cc_final: 0.8417 (mmt) REVERT: A 556 ARG cc_start: 0.7180 (mtp-110) cc_final: 0.6956 (mtp-110) outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 0.2567 time to fit residues: 17.2928 Evaluate side-chains 41 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 236 HIS Chi-restraints excluded: chain A residue 364 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN A 494 GLN A 623 GLN A 703 ASN A 729 GLN A 756 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.058635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.040447 restraints weight = 18043.322| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 3.51 r_work: 0.2591 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5366 Z= 0.230 Angle : 0.557 5.750 7273 Z= 0.287 Chirality : 0.043 0.127 817 Planarity : 0.005 0.046 950 Dihedral : 6.893 57.105 752 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.94 % Allowed : 7.41 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.29), residues: 660 helix: -2.37 (0.28), residues: 256 sheet: -1.45 (0.52), residues: 94 loop : -1.86 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 709 HIS 0.002 0.001 HIS A 179 PHE 0.010 0.001 PHE A 625 TYR 0.018 0.001 TYR A 292 ARG 0.002 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 389 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8677 (mp0) outliers start: 11 outliers final: 7 residues processed: 44 average time/residue: 0.2388 time to fit residues: 13.2692 Evaluate side-chains 42 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 236 HIS Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 777 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.058719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.040374 restraints weight = 18222.676| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.55 r_work: 0.2586 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5366 Z= 0.205 Angle : 0.513 5.358 7273 Z= 0.258 Chirality : 0.042 0.126 817 Planarity : 0.005 0.041 950 Dihedral : 6.181 59.388 747 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.12 % Allowed : 9.70 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.31), residues: 660 helix: -1.27 (0.32), residues: 260 sheet: -1.23 (0.51), residues: 94 loop : -1.53 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 709 HIS 0.004 0.001 HIS A 236 PHE 0.008 0.001 PHE A 194 TYR 0.013 0.001 TYR A 292 ARG 0.002 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 292 TYR cc_start: 0.9046 (t80) cc_final: 0.8809 (t80) REVERT: A 389 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8737 (mp0) REVERT: A 776 CYS cc_start: 0.8972 (m) cc_final: 0.8703 (p) outliers start: 12 outliers final: 8 residues processed: 44 average time/residue: 0.2318 time to fit residues: 13.1788 Evaluate side-chains 42 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 236 HIS Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 777 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 41 optimal weight: 0.0970 chunk 13 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 66 optimal weight: 0.0770 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.059293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.041049 restraints weight = 18404.806| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 3.49 r_work: 0.2609 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5366 Z= 0.153 Angle : 0.479 5.400 7273 Z= 0.241 Chirality : 0.041 0.124 817 Planarity : 0.004 0.040 950 Dihedral : 5.783 58.070 747 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.94 % Allowed : 9.52 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.32), residues: 660 helix: -0.56 (0.34), residues: 258 sheet: -0.91 (0.52), residues: 94 loop : -1.16 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 709 HIS 0.006 0.001 HIS A 236 PHE 0.007 0.001 PHE A 710 TYR 0.009 0.001 TYR A 292 ARG 0.001 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 TYR cc_start: 0.9086 (t80) cc_final: 0.8785 (t80) REVERT: A 387 ASP cc_start: 0.8535 (t70) cc_final: 0.8231 (t70) REVERT: A 564 MET cc_start: 0.8259 (mtp) cc_final: 0.8037 (mtp) REVERT: A 776 CYS cc_start: 0.9023 (m) cc_final: 0.8735 (p) outliers start: 11 outliers final: 5 residues processed: 43 average time/residue: 0.2210 time to fit residues: 12.2351 Evaluate side-chains 37 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 702 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 17 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 53 optimal weight: 0.0670 chunk 11 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.057228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.038949 restraints weight = 18352.479| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 3.39 r_work: 0.2567 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5366 Z= 0.187 Angle : 0.478 6.210 7273 Z= 0.239 Chirality : 0.042 0.131 817 Planarity : 0.004 0.046 950 Dihedral : 5.109 59.844 745 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.94 % Allowed : 10.23 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.33), residues: 660 helix: -0.24 (0.34), residues: 261 sheet: -0.66 (0.55), residues: 87 loop : -1.05 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 709 HIS 0.001 0.000 HIS A 179 PHE 0.009 0.001 PHE A 194 TYR 0.006 0.001 TYR A 517 ARG 0.001 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 292 TYR cc_start: 0.9076 (t80) cc_final: 0.8716 (t80) REVERT: A 387 ASP cc_start: 0.8598 (t70) cc_final: 0.8172 (t0) REVERT: A 776 CYS cc_start: 0.9015 (m) cc_final: 0.8747 (p) outliers start: 11 outliers final: 8 residues processed: 42 average time/residue: 0.1968 time to fit residues: 11.0591 Evaluate side-chains 40 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 702 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 61 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.057012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.038734 restraints weight = 18497.441| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.38 r_work: 0.2560 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5366 Z= 0.197 Angle : 0.479 6.486 7273 Z= 0.239 Chirality : 0.042 0.129 817 Planarity : 0.004 0.045 950 Dihedral : 4.766 54.582 745 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.41 % Allowed : 11.46 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.33), residues: 660 helix: 0.12 (0.35), residues: 261 sheet: -0.55 (0.55), residues: 87 loop : -0.94 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 709 HIS 0.001 0.000 HIS A 179 PHE 0.010 0.001 PHE A 194 TYR 0.006 0.001 TYR A 292 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 TYR cc_start: 0.9084 (t80) cc_final: 0.8728 (t80) REVERT: A 387 ASP cc_start: 0.8598 (t70) cc_final: 0.8161 (t70) REVERT: A 776 CYS cc_start: 0.9137 (m) cc_final: 0.8844 (p) outliers start: 8 outliers final: 6 residues processed: 41 average time/residue: 0.2062 time to fit residues: 11.2324 Evaluate side-chains 39 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 702 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 56 optimal weight: 0.0770 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 16 optimal weight: 0.0570 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.059573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.040780 restraints weight = 17998.808| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 3.53 r_work: 0.2606 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5366 Z= 0.151 Angle : 0.468 8.780 7273 Z= 0.232 Chirality : 0.042 0.221 817 Planarity : 0.004 0.044 950 Dihedral : 4.456 52.412 744 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.06 % Allowed : 11.99 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.33), residues: 660 helix: 0.45 (0.35), residues: 259 sheet: -0.45 (0.54), residues: 93 loop : -0.79 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 709 HIS 0.001 0.000 HIS A 179 PHE 0.006 0.001 PHE A 442 TYR 0.006 0.001 TYR A 292 ARG 0.001 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 292 TYR cc_start: 0.9102 (t80) cc_final: 0.8728 (t80) REVERT: A 387 ASP cc_start: 0.8565 (t70) cc_final: 0.8148 (t70) REVERT: A 776 CYS cc_start: 0.9176 (m) cc_final: 0.8857 (p) outliers start: 6 outliers final: 5 residues processed: 41 average time/residue: 0.2110 time to fit residues: 11.5828 Evaluate side-chains 38 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 702 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 28 optimal weight: 5.9990 chunk 33 optimal weight: 0.2980 chunk 43 optimal weight: 0.0270 chunk 64 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 65 optimal weight: 0.0040 overall best weight: 0.8654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.056998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.038581 restraints weight = 18420.109| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 3.37 r_work: 0.2556 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5366 Z= 0.229 Angle : 0.498 8.654 7273 Z= 0.245 Chirality : 0.043 0.227 817 Planarity : 0.005 0.068 950 Dihedral : 4.170 51.383 740 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.76 % Allowed : 11.29 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.33), residues: 660 helix: 0.64 (0.35), residues: 259 sheet: -0.46 (0.54), residues: 93 loop : -0.71 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 709 HIS 0.002 0.001 HIS A 179 PHE 0.024 0.001 PHE A 495 TYR 0.007 0.001 TYR A 292 ARG 0.001 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 387 ASP cc_start: 0.8621 (t70) cc_final: 0.8197 (t70) REVERT: A 776 CYS cc_start: 0.9205 (m) cc_final: 0.8904 (p) outliers start: 10 outliers final: 6 residues processed: 42 average time/residue: 0.1947 time to fit residues: 10.9049 Evaluate side-chains 39 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 702 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 0.0870 chunk 58 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 41 optimal weight: 0.0060 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 0.0060 overall best weight: 0.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.060150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.041369 restraints weight = 17963.527| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 3.52 r_work: 0.2624 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5366 Z= 0.125 Angle : 0.467 8.282 7273 Z= 0.231 Chirality : 0.041 0.220 817 Planarity : 0.005 0.061 950 Dihedral : 3.924 46.651 740 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.88 % Allowed : 12.35 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.34), residues: 660 helix: 0.96 (0.35), residues: 257 sheet: -0.27 (0.55), residues: 93 loop : -0.69 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 709 HIS 0.001 0.000 HIS A 179 PHE 0.006 0.001 PHE A 442 TYR 0.006 0.001 TYR A 292 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 TYR cc_start: 0.9085 (t80) cc_final: 0.8787 (t80) REVERT: A 387 ASP cc_start: 0.8537 (t70) cc_final: 0.8103 (t70) REVERT: A 776 CYS cc_start: 0.9164 (m) cc_final: 0.8872 (p) outliers start: 5 outliers final: 5 residues processed: 38 average time/residue: 0.2203 time to fit residues: 11.1117 Evaluate side-chains 38 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 678 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 65 optimal weight: 0.0270 chunk 4 optimal weight: 0.2980 chunk 12 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.059491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.041006 restraints weight = 18032.780| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 3.48 r_work: 0.2613 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5366 Z= 0.154 Angle : 0.470 8.722 7273 Z= 0.232 Chirality : 0.042 0.223 817 Planarity : 0.005 0.061 950 Dihedral : 3.904 43.800 740 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.06 % Allowed : 12.17 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.34), residues: 660 helix: 1.08 (0.35), residues: 262 sheet: -0.23 (0.55), residues: 93 loop : -0.65 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 363 HIS 0.001 0.000 HIS A 179 PHE 0.023 0.001 PHE A 495 TYR 0.010 0.001 TYR A 334 ARG 0.001 0.000 ARG A 364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 TYR cc_start: 0.9073 (t80) cc_final: 0.8771 (t80) REVERT: A 387 ASP cc_start: 0.8563 (t70) cc_final: 0.8138 (t70) outliers start: 6 outliers final: 6 residues processed: 39 average time/residue: 0.2172 time to fit residues: 11.2859 Evaluate side-chains 39 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 686 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 64 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.058486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.040126 restraints weight = 17918.833| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.41 r_work: 0.2581 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5366 Z= 0.232 Angle : 0.519 8.763 7273 Z= 0.253 Chirality : 0.043 0.219 817 Planarity : 0.005 0.058 950 Dihedral : 4.040 42.209 740 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.06 % Allowed : 12.35 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.34), residues: 660 helix: 1.06 (0.35), residues: 265 sheet: -0.26 (0.55), residues: 93 loop : -0.59 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 363 HIS 0.002 0.001 HIS A 179 PHE 0.010 0.001 PHE A 194 TYR 0.008 0.001 TYR A 334 ARG 0.001 0.000 ARG A 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2761.09 seconds wall clock time: 49 minutes 36.55 seconds (2976.55 seconds total)