Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 14:21:39 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lq6_23482/12_2021/7lq6_23482.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lq6_23482/12_2021/7lq6_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lq6_23482/12_2021/7lq6_23482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lq6_23482/12_2021/7lq6_23482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lq6_23482/12_2021/7lq6_23482.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lq6_23482/12_2021/7lq6_23482.pdb" } resolution = 3.28 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 ------------------------------------------------------------------------------- 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/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: 3.36, per 1000 atoms: 0.64 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 - 3.50 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 778.8 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: 0.39 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: 1.74 Time building geometry restraints manager: 2.18 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: 99.14 - 106.11: 162 106.11 - 113.09: 2876 113.09 - 120.07: 1854 120.07 - 127.05: 2322 127.05 - 134.03: 59 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: 1.55 - 2.22: 5 2.22 - 2.89: 1967 2.89 - 3.56: 6615 3.56 - 4.23: 12060 4.23 - 4.90: 20694 Nonbonded interactions: 41341 Sorted by model distance: nonbonded pdb=" CG ASN A 361 " pdb=" NH1 ARG A 364 " model vdw 1.549 3.350 nonbonded pdb=" ND2 ASN A 361 " pdb=" NH1 ARG A 364 " model vdw 1.733 3.200 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 2.520 nonbonded pdb=" OD1 ASN A 361 " pdb=" NH1 ARG A 364 " model vdw 2.090 2.520 ... (remaining 41336 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 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. 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 Write .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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.240 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.040 Process input model: 18.350 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 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:2.340 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 34.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 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= 0.334 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 : 1.549 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.45 % Favored : 94.39 % Rotamer Outliers : 1.41 % 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 *********************** 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 fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.688 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 0.2529 time to fit residues: 17.1355 Evaluate side-chains 41 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.639 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 6 average time/residue: 0.2852 time to fit residues: 2.7768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 0.0020 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 5366 Z= 0.254 Angle : 0.565 5.308 7273 Z= 0.290 Chirality : 0.044 0.127 817 Planarity : 0.006 0.118 950 Dihedral : 4.342 19.968 736 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.07 (0.29), residues: 660 helix: -2.38 (0.28), residues: 259 sheet: -1.24 (0.58), residues: 80 loop : -1.85 (0.31), residues: 321 *********************** 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 47 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 45 average time/residue: 0.1919 time to fit residues: 11.6417 Evaluate side-chains 41 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.625 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1321 time to fit residues: 2.1319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 0.0270 chunk 16 optimal weight: 0.0770 chunk 60 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 5366 Z= 0.136 Angle : 0.482 5.935 7273 Z= 0.241 Chirality : 0.041 0.124 817 Planarity : 0.006 0.118 950 Dihedral : 3.893 18.887 736 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 0.88 % 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: -2.08 (0.31), residues: 660 helix: -1.21 (0.32), residues: 259 sheet: -1.14 (0.53), residues: 87 loop : -1.49 (0.33), residues: 314 *********************** 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 41 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.647 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 41 average time/residue: 0.1798 time to fit residues: 10.1908 Evaluate side-chains 35 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.636 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0552 time to fit residues: 1.1058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 64 optimal weight: 0.0370 chunk 57 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN A 705 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2282 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= 0.263 Angle : 0.533 7.544 7273 Z= 0.265 Chirality : 0.043 0.136 817 Planarity : 0.006 0.133 950 Dihedral : 3.954 18.125 736 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 1.23 % 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: -1.52 (0.32), residues: 660 helix: -0.66 (0.34), residues: 260 sheet: -0.79 (0.54), residues: 87 loop : -1.29 (0.34), residues: 313 *********************** 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 41 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.613 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 38 average time/residue: 0.1786 time to fit residues: 9.3109 Evaluate side-chains 36 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.574 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0641 time to fit residues: 1.3015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 0.0030 chunk 38 optimal weight: 0.7980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 5366 Z= 0.163 Angle : 0.479 6.654 7273 Z= 0.239 Chirality : 0.041 0.125 817 Planarity : 0.006 0.136 950 Dihedral : 3.754 18.668 736 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.35 % 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: -1.16 (0.33), residues: 660 helix: -0.30 (0.34), residues: 260 sheet: -0.56 (0.55), residues: 87 loop : -1.15 (0.34), residues: 313 *********************** 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 35 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.599 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 0.1592 time to fit residues: 8.0914 Evaluate side-chains 32 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.643 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0516 time to fit residues: 0.9691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 30 optimal weight: 0.0770 chunk 5 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 0.0010 overall best weight: 0.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2672 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= 0.149 Angle : 0.469 6.576 7273 Z= 0.234 Chirality : 0.041 0.124 817 Planarity : 0.005 0.109 950 Dihedral : 3.657 17.534 736 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.53 % 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: -0.84 (0.33), residues: 660 helix: -0.03 (0.34), residues: 262 sheet: -0.35 (0.56), residues: 87 loop : -0.99 (0.34), residues: 311 *********************** 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 37 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.623 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 37 average time/residue: 0.1500 time to fit residues: 8.0511 Evaluate side-chains 32 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.620 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 5366 Z= 0.192 Angle : 0.511 9.575 7273 Z= 0.253 Chirality : 0.042 0.236 817 Planarity : 0.007 0.157 950 Dihedral : 3.692 18.207 736 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.88 % 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: -0.59 (0.33), residues: 660 helix: 0.24 (0.34), residues: 262 sheet: -0.27 (0.57), residues: 87 loop : -0.90 (0.35), residues: 311 *********************** 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 39 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.634 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 36 average time/residue: 0.1743 time to fit residues: 8.9826 Evaluate side-chains 34 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.652 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0785 time to fit residues: 1.0086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 5366 Z= 0.195 Angle : 0.515 9.765 7273 Z= 0.255 Chirality : 0.042 0.224 817 Planarity : 0.007 0.165 950 Dihedral : 3.695 17.898 736 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.18 % 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: -0.39 (0.33), residues: 660 helix: 0.51 (0.35), residues: 261 sheet: -0.23 (0.58), residues: 86 loop : -0.87 (0.35), residues: 313 *********************** 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 34 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.643 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 34 average time/residue: 0.1556 time to fit residues: 7.7672 Evaluate side-chains 33 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.644 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 0.2980 chunk 56 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 0.0980 chunk 61 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 5366 Z= 0.143 Angle : 0.489 8.458 7273 Z= 0.242 Chirality : 0.041 0.223 817 Planarity : 0.006 0.149 950 Dihedral : 3.607 18.292 736 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.35 % 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: -0.19 (0.34), residues: 660 helix: 0.67 (0.35), residues: 262 sheet: -0.13 (0.58), residues: 86 loop : -0.75 (0.35), residues: 312 *********************** 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 37 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.634 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 37 average time/residue: 0.1652 time to fit residues: 8.7120 Evaluate side-chains 33 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.648 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 0.0070 chunk 5 optimal weight: 0.9980 chunk 41 optimal weight: 0.0470 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 56 optimal weight: 0.0770 chunk 16 optimal weight: 7.9990 chunk 49 optimal weight: 0.2980 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.2454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.079 5366 Z= 0.128 Angle : 0.507 11.683 7273 Z= 0.253 Chirality : 0.041 0.220 817 Planarity : 0.007 0.182 950 Dihedral : 3.496 17.183 736 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.00 % 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: -0.03 (0.34), residues: 660 helix: 0.79 (0.34), residues: 267 sheet: -0.04 (0.56), residues: 93 loop : -0.68 (0.36), residues: 300 ********************** 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 34 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.623 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1527 time to fit residues: 7.7123 Evaluate side-chains 33 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.671 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 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 = 0.3365 r_free = 0.3365 target = 0.061971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.043266 restraints weight = 17915.221| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.60 r_work: 0.2822 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work: 0.2804 rms_B_bonded: 3.37 restraints_weight: 0.1250 r_work: 0.2795 rms_B_bonded: 3.40 restraints_weight: 0.0625 r_work: 0.2785 rms_B_bonded: 3.46 restraints_weight: 0.0312 r_work: 0.2775 rms_B_bonded: 3.53 restraints_weight: 0.0156 r_work: 0.2765 rms_B_bonded: 3.61 restraints_weight: 0.0078 r_work: 0.2755 rms_B_bonded: 3.71 restraints_weight: 0.0039 r_work: 0.2745 rms_B_bonded: 3.82 restraints_weight: 0.0020 r_work: 0.2734 rms_B_bonded: 3.94 restraints_weight: 0.0010 r_work: 0.2723 rms_B_bonded: 4.08 restraints_weight: 0.0005 r_work: 0.2712 rms_B_bonded: 4.24 restraints_weight: 0.0002 r_work: 0.2700 rms_B_bonded: 4.40 restraints_weight: 0.0001 r_work: 0.2688 rms_B_bonded: 4.59 restraints_weight: 0.0001 r_work: 0.2676 rms_B_bonded: 4.79 restraints_weight: 0.0000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 5366 Z= 0.203 Angle : 0.537 9.681 7273 Z= 0.264 Chirality : 0.042 0.219 817 Planarity : 0.007 0.167 950 Dihedral : 3.641 17.988 736 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.00 % 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: 1.01 (0.35), residues: 261 sheet: 0.02 (0.56), residues: 93 loop : -0.67 (0.35), residues: 306 =============================================================================== Job complete usr+sys time: 1420.76 seconds wall clock time: 26 minutes 26.14 seconds (1586.14 seconds total)