Starting phenix.real_space_refine on Fri Mar 15 22:33:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xci_33121/03_2024/7xci_33121.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xci_33121/03_2024/7xci_33121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xci_33121/03_2024/7xci_33121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xci_33121/03_2024/7xci_33121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xci_33121/03_2024/7xci_33121.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xci_33121/03_2024/7xci_33121.pdb" } resolution = 3.2 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= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6463 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4189 2.51 5 N 1079 2.21 5 O 1241 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6547 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 Chain: "B" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1565 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.95, per 1000 atoms: 0.91 Number of scatterers: 6547 At special positions: 0 Unit cell: (77.22, 99.66, 114.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1241 8.00 N 1079 7.00 C 4189 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 702 " - " ASN A 432 " " NAG A 703 " - " ASN A 53 " " NAG A 704 " - " ASN A 90 " " NAG A 705 " - " ASN A 322 " " NAG A 706 " - " ASN A 103 " " NAG B 601 " - " ASN B 343 " " NAG C 1 " - " ASN A 546 " Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 56.5% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.598A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 92 through 102 removed outlier: 3.847A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.531A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 172 through 194 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.807A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.718A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.708A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.601A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.737A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.919A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 444 removed outlier: 3.650A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 466 removed outlier: 3.831A pdb=" N THR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 4.531A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.854A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.564A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.866A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.680A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 600 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.087A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.872A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.887A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 305 hydrogen bonds defined for protein. 872 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: 1.77 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.24: 670 1.24 - 1.39: 2133 1.39 - 1.54: 3845 1.54 - 1.69: 25 1.69 - 1.85: 59 Bond restraints: 6732 Sorted by residual: bond pdb=" CG PRO A 469 " pdb=" CD PRO A 469 " ideal model delta sigma weight residual 1.503 1.084 0.419 3.40e-02 8.65e+02 1.52e+02 bond pdb=" CG PRO A 263 " pdb=" CD PRO A 263 " ideal model delta sigma weight residual 1.503 1.103 0.400 3.40e-02 8.65e+02 1.39e+02 bond pdb=" N PRO A 469 " pdb=" CD PRO A 469 " ideal model delta sigma weight residual 1.473 1.549 -0.076 1.40e-02 5.10e+03 2.92e+01 bond pdb=" N PRO A 263 " pdb=" CD PRO A 263 " ideal model delta sigma weight residual 1.473 1.541 -0.068 1.40e-02 5.10e+03 2.34e+01 bond pdb=" CB PRO A 469 " pdb=" CG PRO A 469 " ideal model delta sigma weight residual 1.492 1.704 -0.212 5.00e-02 4.00e+02 1.81e+01 ... (remaining 6727 not shown) Histogram of bond angle deviations from ideal: 82.34 - 92.67: 4 92.67 - 103.00: 53 103.00 - 113.33: 3655 113.33 - 123.66: 5243 123.66 - 134.00: 198 Bond angle restraints: 9153 Sorted by residual: angle pdb=" N PRO A 263 " pdb=" CD PRO A 263 " pdb=" CG PRO A 263 " ideal model delta sigma weight residual 103.20 82.34 20.86 1.50e+00 4.44e-01 1.93e+02 angle pdb=" N PRO A 469 " pdb=" CD PRO A 469 " pdb=" CG PRO A 469 " ideal model delta sigma weight residual 103.20 82.45 20.75 1.50e+00 4.44e-01 1.91e+02 angle pdb=" CA PRO A 263 " pdb=" CB PRO A 263 " pdb=" CG PRO A 263 " ideal model delta sigma weight residual 104.50 90.21 14.29 1.90e+00 2.77e-01 5.65e+01 angle pdb=" CA PRO A 469 " pdb=" CB PRO A 469 " pdb=" CG PRO A 469 " ideal model delta sigma weight residual 104.50 91.08 13.42 1.90e+00 2.77e-01 4.99e+01 angle pdb=" CA PRO A 469 " pdb=" N PRO A 469 " pdb=" CD PRO A 469 " ideal model delta sigma weight residual 112.00 102.73 9.27 1.40e+00 5.10e-01 4.38e+01 ... (remaining 9148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 3698 17.63 - 35.26: 299 35.26 - 52.89: 66 52.89 - 70.52: 9 70.52 - 88.15: 8 Dihedral angle restraints: 4080 sinusoidal: 1750 harmonic: 2330 Sorted by residual: dihedral pdb=" CA PRO B 337 " pdb=" C PRO B 337 " pdb=" N PHE B 338 " pdb=" CA PHE B 338 " ideal model delta harmonic sigma weight residual 180.00 154.21 25.79 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 135.79 -42.79 1 1.00e+01 1.00e-02 2.56e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 56.69 36.31 1 1.00e+01 1.00e-02 1.86e+01 ... (remaining 4077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 669 0.038 - 0.076: 232 0.076 - 0.114: 63 0.114 - 0.152: 12 0.152 - 0.190: 4 Chirality restraints: 980 Sorted by residual: chirality pdb=" C1 NAG A 705 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG A 705 " pdb=" O5 NAG A 705 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CA PRO B 373 " pdb=" N PRO B 373 " pdb=" C PRO B 373 " pdb=" CB PRO B 373 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" C2 NAG C 2 " pdb=" C1 NAG C 2 " pdb=" C3 NAG C 2 " pdb=" N2 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 977 not shown) Planarity restraints: 1183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 468 " -0.072 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO A 469 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 469 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 469 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 262 " -0.059 5.00e-02 4.00e+02 8.31e-02 1.10e+01 pdb=" N PRO A 263 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 263 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 263 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 414 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO A 415 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " -0.031 5.00e-02 4.00e+02 ... (remaining 1180 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 43 2.58 - 3.16: 5341 3.16 - 3.74: 9924 3.74 - 4.32: 13728 4.32 - 4.90: 23220 Nonbonded interactions: 52256 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.000 2.230 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.265 2.440 nonbonded pdb=" OG SER A 607 " pdb=" OD1 ASP A 609 " model vdw 2.272 2.440 nonbonded pdb=" OG SER A 77 " pdb=" O GLN A 101 " model vdw 2.304 2.440 nonbonded pdb=" OE1 GLU A 189 " pdb=" NH2 ARG A 192 " model vdw 2.310 2.520 ... (remaining 52251 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=0.49 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: 6.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 27.570 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 25.640 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 : 0.009 0.419 6732 Z= 0.584 Angle : 0.753 20.857 9153 Z= 0.446 Chirality : 0.043 0.190 980 Planarity : 0.006 0.102 1176 Dihedral : 13.674 88.150 2563 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.30 % Favored : 96.44 % Rotamer: Outliers : 0.14 % Allowed : 0.57 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.57 (0.30), residues: 788 helix: 1.09 (0.27), residues: 387 sheet: 1.23 (0.73), residues: 50 loop : -0.50 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 165 HIS 0.006 0.001 HIS A 378 PHE 0.022 0.001 PHE A 504 TYR 0.018 0.001 TYR A 202 ARG 0.007 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.753 Fit side-chains REVERT: A 383 MET cc_start: 0.8242 (mtp) cc_final: 0.7894 (mtp) REVERT: B 420 ASP cc_start: 0.8031 (m-30) cc_final: 0.7576 (m-30) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 0.1814 time to fit residues: 24.8920 Evaluate side-chains 88 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6732 Z= 0.220 Angle : 0.564 9.557 9153 Z= 0.290 Chirality : 0.043 0.242 980 Planarity : 0.005 0.055 1176 Dihedral : 5.754 55.951 1031 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.30 % Favored : 96.44 % Rotamer: Outliers : 0.57 % Allowed : 6.74 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.66 (0.30), residues: 788 helix: 1.20 (0.27), residues: 387 sheet: 0.69 (0.68), residues: 60 loop : -0.43 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 165 HIS 0.004 0.001 HIS A 34 PHE 0.029 0.001 PHE A 504 TYR 0.020 0.001 TYR A 381 ARG 0.005 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.698 Fit side-chains REVERT: A 435 GLU cc_start: 0.7339 (mp0) cc_final: 0.7082 (mp0) REVERT: B 420 ASP cc_start: 0.8097 (m-30) cc_final: 0.7618 (m-30) outliers start: 4 outliers final: 2 residues processed: 94 average time/residue: 0.1690 time to fit residues: 22.0657 Evaluate side-chains 87 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 468 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 0.0870 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 56 optimal weight: 0.3980 chunk 53 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6732 Z= 0.170 Angle : 0.508 9.597 9153 Z= 0.262 Chirality : 0.042 0.249 980 Planarity : 0.004 0.053 1176 Dihedral : 5.211 55.707 1031 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.92 % Favored : 96.82 % Rotamer: Outliers : 1.43 % Allowed : 8.46 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.83 (0.30), residues: 788 helix: 1.44 (0.27), residues: 381 sheet: 0.75 (0.68), residues: 60 loop : -0.45 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 165 HIS 0.003 0.001 HIS A 34 PHE 0.024 0.001 PHE A 504 TYR 0.017 0.001 TYR A 381 ARG 0.004 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.786 Fit side-chains REVERT: B 420 ASP cc_start: 0.8116 (m-30) cc_final: 0.7727 (m-30) outliers start: 10 outliers final: 5 residues processed: 94 average time/residue: 0.1686 time to fit residues: 22.2030 Evaluate side-chains 86 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6732 Z= 0.182 Angle : 0.536 9.658 9153 Z= 0.271 Chirality : 0.042 0.250 980 Planarity : 0.004 0.045 1176 Dihedral : 5.215 55.579 1031 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer: Outliers : 1.15 % Allowed : 10.33 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: 0.82 (0.30), residues: 788 helix: 1.47 (0.27), residues: 381 sheet: 0.71 (0.68), residues: 60 loop : -0.49 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 165 HIS 0.003 0.001 HIS A 34 PHE 0.021 0.001 PHE A 504 TYR 0.019 0.001 TYR A 381 ARG 0.003 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.747 Fit side-chains REVERT: B 360 ASN cc_start: 0.7197 (m-40) cc_final: 0.6894 (m-40) REVERT: B 420 ASP cc_start: 0.8125 (m-30) cc_final: 0.7748 (m-30) outliers start: 8 outliers final: 3 residues processed: 89 average time/residue: 0.1726 time to fit residues: 21.3207 Evaluate side-chains 86 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.0370 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 0.0470 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.0980 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 0.0370 chunk 25 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 397 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6732 Z= 0.150 Angle : 0.508 9.616 9153 Z= 0.257 Chirality : 0.041 0.242 980 Planarity : 0.004 0.044 1176 Dihedral : 4.975 55.608 1031 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 1.43 % Allowed : 10.76 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.00 (0.31), residues: 788 helix: 1.71 (0.27), residues: 373 sheet: 0.74 (0.69), residues: 60 loop : -0.45 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 165 HIS 0.003 0.001 HIS A 34 PHE 0.023 0.001 PHE A 504 TYR 0.017 0.001 TYR A 202 ARG 0.004 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.739 Fit side-chains REVERT: A 435 GLU cc_start: 0.7526 (mp0) cc_final: 0.7194 (mp0) REVERT: B 360 ASN cc_start: 0.7273 (m-40) cc_final: 0.6804 (t0) REVERT: B 420 ASP cc_start: 0.8103 (m-30) cc_final: 0.7699 (m-30) outliers start: 10 outliers final: 8 residues processed: 92 average time/residue: 0.1767 time to fit residues: 22.3324 Evaluate side-chains 90 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6732 Z= 0.199 Angle : 0.539 9.629 9153 Z= 0.272 Chirality : 0.042 0.246 980 Planarity : 0.004 0.045 1176 Dihedral : 5.013 55.398 1031 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 1.58 % Allowed : 11.05 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.98 (0.31), residues: 788 helix: 1.71 (0.27), residues: 373 sheet: 0.66 (0.69), residues: 60 loop : -0.46 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 165 HIS 0.004 0.001 HIS A 34 PHE 0.022 0.001 PHE A 504 TYR 0.023 0.001 TYR A 381 ARG 0.007 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.802 Fit side-chains REVERT: B 360 ASN cc_start: 0.7228 (m-40) cc_final: 0.6766 (t0) REVERT: B 420 ASP cc_start: 0.8122 (m-30) cc_final: 0.7732 (m-30) outliers start: 11 outliers final: 7 residues processed: 93 average time/residue: 0.1845 time to fit residues: 23.4184 Evaluate side-chains 90 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 chunk 75 optimal weight: 0.9990 chunk 47 optimal weight: 0.0870 chunk 45 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6732 Z= 0.174 Angle : 0.517 9.608 9153 Z= 0.263 Chirality : 0.042 0.246 980 Planarity : 0.004 0.046 1176 Dihedral : 4.962 55.549 1031 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer: Outliers : 1.15 % Allowed : 11.76 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.03 (0.31), residues: 788 helix: 1.72 (0.27), residues: 374 sheet: 0.59 (0.68), residues: 60 loop : -0.41 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 165 HIS 0.005 0.001 HIS A 265 PHE 0.020 0.001 PHE A 504 TYR 0.016 0.001 TYR A 381 ARG 0.007 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.690 Fit side-chains REVERT: B 360 ASN cc_start: 0.7220 (m-40) cc_final: 0.6806 (t0) REVERT: B 420 ASP cc_start: 0.8104 (m-30) cc_final: 0.7701 (m-30) outliers start: 8 outliers final: 7 residues processed: 87 average time/residue: 0.1825 time to fit residues: 21.6262 Evaluate side-chains 88 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 0.0010 chunk 68 optimal weight: 0.0040 chunk 72 optimal weight: 0.1980 chunk 65 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 290 ASN A 397 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6732 Z= 0.126 Angle : 0.491 9.578 9153 Z= 0.248 Chirality : 0.041 0.232 980 Planarity : 0.004 0.045 1176 Dihedral : 4.671 55.602 1031 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.18 % Favored : 96.70 % Rotamer: Outliers : 1.00 % Allowed : 12.20 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.19 (0.31), residues: 788 helix: 1.92 (0.27), residues: 373 sheet: 0.61 (0.67), residues: 60 loop : -0.37 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 165 HIS 0.004 0.001 HIS A 374 PHE 0.021 0.001 PHE A 504 TYR 0.017 0.001 TYR A 202 ARG 0.009 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.696 Fit side-chains REVERT: B 360 ASN cc_start: 0.7153 (m-40) cc_final: 0.6788 (t0) REVERT: B 420 ASP cc_start: 0.8092 (m-30) cc_final: 0.7705 (m-30) outliers start: 7 outliers final: 5 residues processed: 91 average time/residue: 0.1785 time to fit residues: 22.0116 Evaluate side-chains 85 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.3980 chunk 55 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 0.0980 chunk 45 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 290 ASN A 397 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6732 Z= 0.166 Angle : 0.533 9.681 9153 Z= 0.267 Chirality : 0.041 0.233 980 Planarity : 0.004 0.053 1176 Dihedral : 4.733 55.475 1031 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.18 % Favored : 96.70 % Rotamer: Outliers : 1.15 % Allowed : 12.34 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.20 (0.31), residues: 788 helix: 1.91 (0.27), residues: 375 sheet: 0.49 (0.67), residues: 59 loop : -0.33 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 PHE 0.022 0.001 PHE A 504 TYR 0.018 0.001 TYR A 202 ARG 0.013 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.704 Fit side-chains REVERT: B 420 ASP cc_start: 0.8105 (m-30) cc_final: 0.7691 (m-30) outliers start: 8 outliers final: 6 residues processed: 87 average time/residue: 0.1819 time to fit residues: 21.5658 Evaluate side-chains 86 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 0.0070 chunk 49 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 397 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6732 Z= 0.172 Angle : 0.552 11.666 9153 Z= 0.274 Chirality : 0.042 0.239 980 Planarity : 0.004 0.051 1176 Dihedral : 4.783 55.421 1031 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 1.15 % Allowed : 12.77 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.21 (0.31), residues: 788 helix: 1.91 (0.27), residues: 375 sheet: 0.43 (0.67), residues: 59 loop : -0.31 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 165 HIS 0.003 0.001 HIS A 34 PHE 0.022 0.001 PHE A 504 TYR 0.018 0.001 TYR A 381 ARG 0.012 0.000 ARG A 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.735 Fit side-chains REVERT: B 420 ASP cc_start: 0.8093 (m-30) cc_final: 0.7660 (m-30) outliers start: 8 outliers final: 7 residues processed: 88 average time/residue: 0.1783 time to fit residues: 21.4703 Evaluate side-chains 87 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 54 optimal weight: 0.0060 chunk 3 optimal weight: 0.0170 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 overall best weight: 0.4434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 397 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.177196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.120005 restraints weight = 12339.508| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.28 r_work: 0.3170 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6732 Z= 0.156 Angle : 0.529 9.448 9153 Z= 0.265 Chirality : 0.041 0.246 980 Planarity : 0.004 0.052 1176 Dihedral : 4.766 55.510 1031 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 1.29 % Allowed : 12.77 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.21 (0.31), residues: 788 helix: 1.94 (0.27), residues: 375 sheet: 0.41 (0.67), residues: 59 loop : -0.35 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 165 HIS 0.003 0.001 HIS A 34 PHE 0.021 0.001 PHE A 504 TYR 0.018 0.001 TYR A 202 ARG 0.012 0.000 ARG A 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2227.76 seconds wall clock time: 41 minutes 0.57 seconds (2460.57 seconds total)