Starting phenix.real_space_refine on Thu Mar 6 07:20:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lq6_23482/03_2025/7lq6_23482.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lq6_23482/03_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_23482/03_2025/7lq6_23482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lq6_23482/03_2025/7lq6_23482.map" model { file = "/net/cci-nas-00/data/ceres_data/7lq6_23482/03_2025/7lq6_23482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lq6_23482/03_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-5624/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: 4.28, per 1000 atoms: 0.81 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: 1.38 Conformation dependent library (CDL) restraints added in 680.6 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: 0.69 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: 1.62 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.620 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.410 ------------------------------------------------------------------------------- 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 : 0.647 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: 0.2630 time to fit residues: 17.5801 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 : 0.646 ------------------------------------------------------------------------------- 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 = 0.3270 r_free = 0.3270 target = 0.058699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.040437 restraints weight = 18054.119| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 3.52 r_work: 0.2591 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 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 : 0.582 Fit side-chains revert: symmetry clash REVERT: A 389 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8682 (mp0) outliers start: 11 outliers final: 7 residues processed: 44 average time/residue: 0.2470 time to fit residues: 13.7640 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 : 0.639 ------------------------------------------------------------------------------- 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: 4.9990 chunk 53 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 46 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3278 r_free = 0.3278 target = 0.059058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.040779 restraints weight = 18192.392| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.49 r_work: 0.2600 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2115 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= 0.179 Angle : 0.501 5.230 7273 Z= 0.252 Chirality : 0.042 0.125 817 Planarity : 0.005 0.041 950 Dihedral : 6.042 57.801 747 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.94 % Allowed : 10.05 % Favored : 88.01 % 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: -2.11 (0.31), residues: 660 helix: -1.22 (0.32), residues: 260 sheet: -1.22 (0.51), residues: 94 loop : -1.50 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 709 HIS 0.003 0.001 HIS A 236 PHE 0.007 0.001 PHE A 194 TYR 0.012 0.001 TYR A 292 ARG 0.002 0.000 ARG A 235 *********************** 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 43 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 292 TYR cc_start: 0.9048 (t80) cc_final: 0.8824 (t80) REVERT: A 389 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8725 (mp0) REVERT: A 776 CYS cc_start: 0.8897 (m) cc_final: 0.8625 (p) outliers start: 11 outliers final: 7 residues processed: 42 average time/residue: 0.2406 time to fit residues: 13.0676 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 : 0.593 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 13 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 66 optimal weight: 0.0670 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 = 0.3270 r_free = 0.3270 target = 0.058768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.040444 restraints weight = 18491.374| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.49 r_work: 0.2589 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2298 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 : 0.497 5.676 7273 Z= 0.250 Chirality : 0.042 0.125 817 Planarity : 0.004 0.041 950 Dihedral : 5.836 59.689 747 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.29 % Allowed : 8.82 % Favored : 88.89 % 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: -1.51 (0.32), residues: 660 helix: -0.63 (0.34), residues: 260 sheet: -0.97 (0.52), residues: 94 loop : -1.23 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 709 HIS 0.006 0.001 HIS A 236 PHE 0.009 0.001 PHE A 194 TYR 0.011 0.001 TYR A 292 ARG 0.002 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 46 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 TYR cc_start: 0.9146 (t80) cc_final: 0.8871 (t80) REVERT: A 387 ASP cc_start: 0.8534 (t70) cc_final: 0.8171 (t70) REVERT: A 776 CYS cc_start: 0.9000 (m) cc_final: 0.8735 (p) outliers start: 13 outliers final: 6 residues processed: 45 average time/residue: 0.2232 time to fit residues: 12.9786 Evaluate side-chains 38 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 468 SER 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: 3.9990 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.0570 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- 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 = 0.3269 r_free = 0.3269 target = 0.058748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.040535 restraints weight = 17927.069| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.43 r_work: 0.2598 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2505 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= 0.182 Angle : 0.476 6.298 7273 Z= 0.238 Chirality : 0.042 0.131 817 Planarity : 0.004 0.046 950 Dihedral : 5.043 57.733 745 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.59 % Allowed : 10.58 % 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: -1.10 (0.33), residues: 660 helix: -0.26 (0.34), residues: 261 sheet: -0.67 (0.55), residues: 87 loop : -1.06 (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 0.007 0.001 TYR A 292 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 42 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 292 TYR cc_start: 0.9127 (t80) cc_final: 0.8789 (t80) REVERT: A 387 ASP cc_start: 0.8549 (t70) cc_final: 0.8139 (t0) REVERT: A 776 CYS cc_start: 0.9041 (m) cc_final: 0.8765 (p) outliers start: 9 outliers final: 6 residues processed: 41 average time/residue: 0.2177 time to fit residues: 11.8209 Evaluate side-chains 40 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 364 ARG 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: 1.9990 chunk 47 optimal weight: 0.3980 chunk 43 optimal weight: 0.0870 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 27 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3249 r_free = 0.3249 target = 0.057734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.039404 restraints weight = 18409.756| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 3.42 r_work: 0.2581 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2696 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= 0.146 Angle : 0.463 6.485 7273 Z= 0.231 Chirality : 0.041 0.125 817 Planarity : 0.004 0.043 950 Dihedral : 4.656 56.683 744 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.41 % Allowed : 11.11 % Favored : 87.48 % 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: -0.68 (0.33), residues: 660 helix: 0.10 (0.34), residues: 261 sheet: -0.48 (0.56), residues: 87 loop : -0.82 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 709 HIS 0.001 0.000 HIS A 179 PHE 0.006 0.001 PHE A 194 TYR 0.010 0.001 TYR A 292 ARG 0.001 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 43 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 TYR cc_start: 0.9101 (t80) cc_final: 0.8752 (t80) REVERT: A 387 ASP cc_start: 0.8606 (t70) cc_final: 0.8183 (t0) REVERT: A 776 CYS cc_start: 0.9082 (m) cc_final: 0.8809 (p) outliers start: 8 outliers final: 6 residues processed: 43 average time/residue: 0.1963 time to fit residues: 11.2411 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 : 0.629 ------------------------------------------------------------------------------- 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: 0.7980 chunk 62 optimal weight: 0.0980 chunk 56 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3241 r_free = 0.3241 target = 0.058061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.040047 restraints weight = 17992.873| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.42 r_work: 0.2581 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2786 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= 0.156 Angle : 0.473 9.155 7273 Z= 0.234 Chirality : 0.042 0.239 817 Planarity : 0.005 0.061 950 Dihedral : 4.472 53.153 744 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.76 % Allowed : 12.17 % Favored : 86.07 % 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: -0.49 (0.33), residues: 660 helix: 0.35 (0.34), residues: 262 sheet: -0.37 (0.56), residues: 87 loop : -0.82 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 709 HIS 0.001 0.000 HIS A 179 PHE 0.023 0.001 PHE A 495 TYR 0.011 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 44 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 292 TYR cc_start: 0.9174 (t80) cc_final: 0.8832 (t80) REVERT: A 387 ASP cc_start: 0.8568 (t70) cc_final: 0.8160 (t70) REVERT: A 776 CYS cc_start: 0.9119 (m) cc_final: 0.8806 (p) outliers start: 10 outliers final: 6 residues processed: 43 average time/residue: 0.1810 time to fit residues: 10.6905 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 chunk 43 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 2 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.3203 r_free = 0.3203 target = 0.056520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.038644 restraints weight = 18247.972| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 3.37 r_work: 0.2531 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 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 : 0.005 0.053 5366 Z= 0.318 Angle : 0.544 9.244 7273 Z= 0.269 Chirality : 0.044 0.232 817 Planarity : 0.005 0.056 950 Dihedral : 4.326 50.832 740 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.94 % Allowed : 11.82 % Favored : 86.24 % 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: -0.50 (0.33), residues: 660 helix: 0.34 (0.34), residues: 268 sheet: -0.50 (0.56), residues: 87 loop : -0.80 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 709 HIS 0.002 0.001 HIS A 179 PHE 0.013 0.001 PHE A 194 TYR 0.010 0.001 TYR A 734 ARG 0.002 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 45 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 292 TYR cc_start: 0.9127 (t80) cc_final: 0.8740 (t80) REVERT: A 387 ASP cc_start: 0.8573 (t70) cc_final: 0.8173 (t70) REVERT: A 776 CYS cc_start: 0.9221 (m) cc_final: 0.8955 (p) outliers start: 11 outliers final: 7 residues processed: 43 average time/residue: 0.2016 time to fit residues: 11.5400 Evaluate side-chains 41 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.3893 > 50: distance: 65 - 68: 7.824 distance: 69 - 70: 8.341 distance: 69 - 72: 13.691 distance: 70 - 71: 28.040 distance: 70 - 75: 4.234 distance: 72 - 73: 11.855 distance: 72 - 74: 15.912 distance: 75 - 76: 4.560 distance: 76 - 77: 9.548 distance: 76 - 79: 3.126 distance: 77 - 78: 17.854 distance: 77 - 83: 10.826 distance: 79 - 80: 9.756 distance: 79 - 81: 10.279 distance: 80 - 82: 10.169 distance: 83 - 84: 18.877 distance: 84 - 85: 15.238 distance: 84 - 87: 11.088 distance: 85 - 86: 6.191 distance: 85 - 90: 19.082 distance: 87 - 88: 27.269 distance: 87 - 89: 12.253 distance: 90 - 91: 21.691 distance: 91 - 92: 25.192 distance: 91 - 94: 23.437 distance: 92 - 93: 27.082 distance: 92 - 98: 24.917 distance: 94 - 95: 12.632 distance: 95 - 96: 19.392 distance: 95 - 97: 12.383 distance: 98 - 99: 25.844 distance: 99 - 100: 6.081 distance: 99 - 102: 13.815 distance: 100 - 101: 8.741 distance: 100 - 106: 9.885 distance: 102 - 103: 21.313 distance: 103 - 104: 21.407 distance: 104 - 105: 24.336 distance: 106 - 107: 10.567 distance: 107 - 108: 9.752 distance: 107 - 110: 13.765 distance: 108 - 109: 14.302 distance: 108 - 115: 9.632 distance: 110 - 111: 17.277 distance: 111 - 112: 16.551 distance: 112 - 113: 17.687 distance: 112 - 114: 9.836 distance: 115 - 116: 6.879 distance: 116 - 117: 7.062 distance: 116 - 119: 3.790 distance: 117 - 118: 7.900 distance: 117 - 123: 10.051 distance: 119 - 120: 15.845 distance: 120 - 121: 15.896 distance: 120 - 122: 15.058 distance: 123 - 124: 9.370 distance: 124 - 125: 5.009 distance: 124 - 127: 4.775 distance: 125 - 126: 16.534 distance: 125 - 131: 8.674 distance: 128 - 130: 7.609 distance: 132 - 133: 5.116 distance: 132 - 135: 5.936 distance: 133 - 134: 25.343 distance: 133 - 142: 7.332 distance: 135 - 136: 15.843 distance: 136 - 137: 11.356 distance: 137 - 138: 22.885 distance: 138 - 139: 11.570 distance: 139 - 140: 24.088 distance: 139 - 141: 27.444 distance: 142 - 143: 5.991 distance: 143 - 144: 10.211 distance: 143 - 146: 9.980 distance: 144 - 145: 15.765 distance: 144 - 151: 5.624 distance: 147 - 148: 11.294 distance: 148 - 149: 3.230 distance: 148 - 150: 6.802