Starting phenix.real_space_refine on Sun Mar 10 20:24:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hg7_34737/03_2024/8hg7_34737_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hg7_34737/03_2024/8hg7_34737.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hg7_34737/03_2024/8hg7_34737_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hg7_34737/03_2024/8hg7_34737_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hg7_34737/03_2024/8hg7_34737_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hg7_34737/03_2024/8hg7_34737.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hg7_34737/03_2024/8hg7_34737.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hg7_34737/03_2024/8hg7_34737_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hg7_34737/03_2024/8hg7_34737_updated.pdb" } resolution = 3.1 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 38 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 3169 2.51 5 N 786 2.21 5 O 813 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 130": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 427": "NH1" <-> "NH2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A ARG 638": "NH1" <-> "NH2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "A ARG 651": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4808 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4532 Classifications: {'peptide': 590} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 562} Chain breaks: 1 Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Unusual residues: {' NA': 1, 'LFL': 1, 'NAG': 1} Classifications: {'undetermined': 3, 'water': 2} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.35, per 1000 atoms: 0.70 Number of scatterers: 4808 At special positions: 0 Unit cell: (74.1469, 74.1469, 95.1736, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 38 16.00 Na 1 11.00 O 813 8.00 N 786 7.00 C 3169 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 511 " distance=2.33 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.41 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 361 " distance=2.30 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 522 " distance=2.28 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 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 934.7 milliseconds 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1124 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 0 sheets defined 72.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 23 through 46 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 78 through 91 removed outlier: 3.535A pdb=" N ALA A 85 " --> pdb=" O PHE A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 119 removed outlier: 3.546A pdb=" N ASN A 101 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 107 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 108 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 109 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 113 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ALA A 114 " --> pdb=" O TRP A 111 " (cutoff:3.500A) Proline residue: A 115 - end of helix Processing helix chain 'A' and resid 125 through 133 removed outlier: 3.606A pdb=" N LEU A 129 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 153 Processing helix chain 'A' and resid 155 through 169 Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 194 through 223 removed outlier: 3.835A pdb=" N VAL A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.635A pdb=" N PHE A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 256 No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 276 through 292 Processing helix chain 'A' and resid 295 through 300 removed outlier: 4.374A pdb=" N ARG A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 320 Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 340 through 343 No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 362 through 373 removed outlier: 4.211A pdb=" N TYR A 366 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Proline residue: A 367 - end of helix removed outlier: 3.819A pdb=" N LEU A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 413 removed outlier: 3.643A pdb=" N THR A 411 " --> pdb=" O MET A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 445 removed outlier: 3.592A pdb=" N VAL A 430 " --> pdb=" O GLY A 426 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) Proline residue: A 442 - end of helix Processing helix chain 'A' and resid 449 through 476 removed outlier: 3.811A pdb=" N LEU A 452 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 453 " --> pdb=" O GLY A 450 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE A 456 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A 457 " --> pdb=" O ASP A 454 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER A 460 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 463 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ALA A 464 " --> pdb=" O SER A 461 " (cutoff:3.500A) Proline residue: A 465 - end of helix removed outlier: 3.522A pdb=" N SER A 468 " --> pdb=" O PRO A 465 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 471 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL A 472 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 475 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE A 476 " --> pdb=" O LEU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 506 removed outlier: 3.596A pdb=" N ARG A 499 " --> pdb=" O MET A 495 " (cutoff:3.500A) Proline residue: A 502 - end of helix removed outlier: 3.983A pdb=" N PHE A 506 " --> pdb=" O PRO A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 522 No H-bonds generated for 'chain 'A' and resid 519 through 522' Processing helix chain 'A' and resid 526 through 547 removed outlier: 3.672A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 555 No H-bonds generated for 'chain 'A' and resid 553 through 555' Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 647 through 671 removed outlier: 3.509A pdb=" N LEU A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 54 288 hydrogen bonds defined for protein. 780 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: 1.28 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 709 1.29 - 1.43: 1412 1.43 - 1.57: 2753 1.57 - 1.72: 1 1.72 - 1.86: 59 Bond restraints: 4934 Sorted by residual: bond pdb=" C MET A 325 " pdb=" O MET A 325 " ideal model delta sigma weight residual 1.237 1.147 0.090 1.19e-02 7.06e+03 5.67e+01 bond pdb=" C PRO A 502 " pdb=" O PRO A 502 " ideal model delta sigma weight residual 1.238 1.149 0.089 1.33e-02 5.65e+03 4.50e+01 bond pdb=" C PRO A 115 " pdb=" O PRO A 115 " ideal model delta sigma weight residual 1.235 1.153 0.082 1.30e-02 5.92e+03 3.94e+01 bond pdb=" C PRO A 324 " pdb=" O PRO A 324 " ideal model delta sigma weight residual 1.238 1.162 0.076 1.33e-02 5.65e+03 3.24e+01 bond pdb=" C TRP A 100 " pdb=" O TRP A 100 " ideal model delta sigma weight residual 1.236 1.308 -0.071 1.29e-02 6.01e+03 3.07e+01 ... (remaining 4929 not shown) Histogram of bond angle deviations from ideal: 94.21 - 102.34: 59 102.34 - 110.48: 1286 110.48 - 118.61: 2807 118.61 - 126.75: 2478 126.75 - 134.88: 98 Bond angle restraints: 6728 Sorted by residual: angle pdb=" N PHE A 113 " pdb=" CA PHE A 113 " pdb=" C PHE A 113 " ideal model delta sigma weight residual 113.55 104.63 8.92 1.26e+00 6.30e-01 5.01e+01 angle pdb=" CA ASP A 261 " pdb=" CB ASP A 261 " pdb=" CG ASP A 261 " ideal model delta sigma weight residual 112.60 119.63 -7.03 1.00e+00 1.00e+00 4.95e+01 angle pdb=" C PHE A 98 " pdb=" CA PHE A 98 " pdb=" CB PHE A 98 " ideal model delta sigma weight residual 110.88 121.59 -10.71 1.57e+00 4.06e-01 4.65e+01 angle pdb=" CA PHE A 148 " pdb=" C PHE A 148 " pdb=" O PHE A 148 " ideal model delta sigma weight residual 120.42 113.58 6.84 1.06e+00 8.90e-01 4.16e+01 angle pdb=" N CYS A 522 " pdb=" CA CYS A 522 " pdb=" C CYS A 522 " ideal model delta sigma weight residual 110.97 118.00 -7.03 1.09e+00 8.42e-01 4.16e+01 ... (remaining 6723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.53: 2622 20.53 - 41.07: 192 41.07 - 61.60: 32 61.60 - 82.13: 4 82.13 - 102.66: 2 Dihedral angle restraints: 2852 sinusoidal: 1088 harmonic: 1764 Sorted by residual: dihedral pdb=" CB CYS A 255 " pdb=" SG CYS A 255 " pdb=" SG CYS A 511 " pdb=" CB CYS A 511 " ideal model delta sinusoidal sigma weight residual -86.00 -21.88 -64.12 1 1.00e+01 1.00e-02 5.41e+01 dihedral pdb=" C PRO A 502 " pdb=" N PRO A 502 " pdb=" CA PRO A 502 " pdb=" CB PRO A 502 " ideal model delta harmonic sigma weight residual -120.70 -134.66 13.96 0 2.50e+00 1.60e-01 3.12e+01 dihedral pdb=" CA GLY A 418 " pdb=" C GLY A 418 " pdb=" N ASP A 419 " pdb=" CA ASP A 419 " ideal model delta harmonic sigma weight residual -180.00 -152.13 -27.87 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 2849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 664 0.132 - 0.263: 115 0.263 - 0.395: 2 0.395 - 0.526: 0 0.526 - 0.658: 1 Chirality restraints: 782 Sorted by residual: chirality pdb=" CA PRO A 502 " pdb=" N PRO A 502 " pdb=" C PRO A 502 " pdb=" CB PRO A 502 " both_signs ideal model delta sigma weight residual False 2.72 2.06 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA PRO A 367 " pdb=" N PRO A 367 " pdb=" C PRO A 367 " pdb=" CB PRO A 367 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA ILE A 251 " pdb=" N ILE A 251 " pdb=" C ILE A 251 " pdb=" CB ILE A 251 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 779 not shown) Planarity restraints: 824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 60 " 0.631 9.50e-02 1.11e+02 2.83e-01 4.89e+01 pdb=" NE ARG A 60 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG A 60 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 60 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 60 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 110 " 0.024 2.00e-02 2.50e+03 4.61e-02 2.12e+01 pdb=" C GLY A 110 " -0.080 2.00e-02 2.50e+03 pdb=" O GLY A 110 " 0.029 2.00e-02 2.50e+03 pdb=" N TRP A 111 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 98 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C PHE A 98 " 0.057 2.00e-02 2.50e+03 pdb=" O PHE A 98 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU A 99 " -0.020 2.00e-02 2.50e+03 ... (remaining 821 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 87 2.68 - 3.23: 4701 3.23 - 3.79: 7630 3.79 - 4.34: 10899 4.34 - 4.90: 17328 Nonbonded interactions: 40645 Sorted by model distance: nonbonded pdb=" O ALA A 73 " pdb="NA NA A 803 " model vdw 2.121 2.470 nonbonded pdb=" O ILE A 76 " pdb="NA NA A 803 " model vdw 2.133 2.470 nonbonded pdb=" ND2 ASN A 250 " pdb=" C1 NAG A 801 " model vdw 2.200 3.550 nonbonded pdb=" OH TYR A 128 " pdb=" O LEU A 559 " model vdw 2.249 2.440 nonbonded pdb=" O ARG A 259 " pdb=" OG SER A 262 " model vdw 2.358 2.440 ... (remaining 40640 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: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.670 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 18.420 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 0.017 0.105 4934 Z= 1.093 Angle : 2.203 13.434 6728 Z= 1.613 Chirality : 0.094 0.658 782 Planarity : 0.012 0.283 824 Dihedral : 14.422 102.661 1716 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.19 % Allowed : 6.36 % Favored : 91.45 % Cbeta Deviations : 0.36 % 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: -2.67 (0.29), residues: 613 helix: -1.54 (0.20), residues: 443 sheet: None (None), residues: 0 loop : -1.90 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP A 487 HIS 0.008 0.002 HIS A 309 PHE 0.022 0.004 PHE A 113 TYR 0.030 0.005 TYR A 128 ARG 0.007 0.001 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.464 Fit side-chains REVERT: A 99 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8147 (mm-30) REVERT: A 104 PHE cc_start: 0.7585 (m-80) cc_final: 0.7376 (m-80) REVERT: A 150 TYR cc_start: 0.8535 (m-10) cc_final: 0.8250 (m-10) REVERT: A 167 GLN cc_start: 0.8475 (tt0) cc_final: 0.8229 (tt0) REVERT: A 191 THR cc_start: 0.8067 (m) cc_final: 0.7826 (m) REVERT: A 216 MET cc_start: 0.8022 (ttp) cc_final: 0.7760 (ttp) REVERT: A 244 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7198 (mm-30) REVERT: A 323 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.7955 (p) REVERT: A 328 MET cc_start: 0.8610 (mtt) cc_final: 0.8222 (mtt) REVERT: A 382 MET cc_start: 0.8263 (mmm) cc_final: 0.8036 (mmm) REVERT: A 412 ARG cc_start: 0.6987 (ttt180) cc_final: 0.5933 (ttp80) REVERT: A 495 MET cc_start: 0.7652 (mtp) cc_final: 0.7261 (mtt) REVERT: A 500 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7392 (tt) REVERT: A 641 GLU cc_start: 0.6454 (mm-30) cc_final: 0.5791 (mt-10) outliers start: 11 outliers final: 5 residues processed: 85 average time/residue: 0.2655 time to fit residues: 26.6598 Evaluate side-chains 76 residues out of total 503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 PRO Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 466 PRO Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 560 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.0870 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN A 399 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4934 Z= 0.166 Angle : 0.614 7.656 6728 Z= 0.316 Chirality : 0.041 0.206 782 Planarity : 0.005 0.037 824 Dihedral : 7.453 97.015 715 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.59 % Allowed : 7.95 % Favored : 90.46 % 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: 0.32 (0.34), residues: 613 helix: 0.83 (0.25), residues: 441 sheet: None (None), residues: 0 loop : -1.27 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 42 HIS 0.002 0.001 HIS A 80 PHE 0.007 0.001 PHE A 165 TYR 0.027 0.001 TYR A 256 ARG 0.004 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.516 Fit side-chains REVERT: A 150 TYR cc_start: 0.8316 (m-10) cc_final: 0.7631 (m-10) REVERT: A 198 MET cc_start: 0.7805 (mtt) cc_final: 0.7602 (mtt) REVERT: A 216 MET cc_start: 0.7983 (ttp) cc_final: 0.7591 (ttp) REVERT: A 244 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7105 (mm-30) REVERT: A 323 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8149 (p) REVERT: A 382 MET cc_start: 0.7988 (mmm) cc_final: 0.7720 (mmm) REVERT: A 412 ARG cc_start: 0.7099 (ttt180) cc_final: 0.5926 (tmt-80) REVERT: A 553 ARG cc_start: 0.7440 (mtp-110) cc_final: 0.6989 (ttp80) REVERT: A 569 GLU cc_start: 0.8204 (tp30) cc_final: 0.7625 (mp0) outliers start: 8 outliers final: 5 residues processed: 76 average time/residue: 0.2289 time to fit residues: 21.3160 Evaluate side-chains 66 residues out of total 503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 517 CYS Chi-restraints excluded: chain A residue 642 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 54 optimal weight: 0.3980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4934 Z= 0.299 Angle : 0.647 7.331 6728 Z= 0.335 Chirality : 0.044 0.176 782 Planarity : 0.006 0.044 824 Dihedral : 7.045 98.776 704 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.99 % Allowed : 10.93 % Favored : 87.08 % 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: 0.57 (0.34), residues: 613 helix: 1.03 (0.25), residues: 439 sheet: None (None), residues: 0 loop : -1.23 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 487 HIS 0.003 0.001 HIS A 555 PHE 0.013 0.002 PHE A 666 TYR 0.019 0.002 TYR A 256 ARG 0.003 0.001 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.488 Fit side-chains REVERT: A 150 TYR cc_start: 0.8319 (m-10) cc_final: 0.7660 (m-10) REVERT: A 216 MET cc_start: 0.8095 (ttp) cc_final: 0.7863 (ttp) REVERT: A 244 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7250 (mm-30) REVERT: A 412 ARG cc_start: 0.6934 (ttt180) cc_final: 0.5770 (tmt-80) REVERT: A 569 GLU cc_start: 0.8382 (tp30) cc_final: 0.7734 (mp0) outliers start: 10 outliers final: 6 residues processed: 69 average time/residue: 0.2253 time to fit residues: 19.1933 Evaluate side-chains 66 residues out of total 503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 642 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 15 optimal weight: 0.0270 chunk 49 optimal weight: 9.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4934 Z= 0.157 Angle : 0.549 7.727 6728 Z= 0.278 Chirality : 0.039 0.160 782 Planarity : 0.005 0.043 824 Dihedral : 6.482 97.523 703 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.59 % Allowed : 12.72 % Favored : 85.69 % 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: 1.02 (0.35), residues: 613 helix: 1.31 (0.25), residues: 445 sheet: None (None), residues: 0 loop : -0.96 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 487 HIS 0.002 0.000 HIS A 555 PHE 0.007 0.001 PHE A 520 TYR 0.020 0.001 TYR A 256 ARG 0.002 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.457 Fit side-chains REVERT: A 91 SER cc_start: 0.8512 (m) cc_final: 0.8054 (p) REVERT: A 150 TYR cc_start: 0.8296 (m-10) cc_final: 0.7591 (m-10) REVERT: A 216 MET cc_start: 0.8082 (ttp) cc_final: 0.7759 (ttp) REVERT: A 412 ARG cc_start: 0.7101 (ttt180) cc_final: 0.5967 (tmt-80) REVERT: A 553 ARG cc_start: 0.7415 (mtp-110) cc_final: 0.6912 (ttp80) REVERT: A 569 GLU cc_start: 0.8292 (tp30) cc_final: 0.7672 (mp0) outliers start: 8 outliers final: 7 residues processed: 70 average time/residue: 0.2343 time to fit residues: 19.9170 Evaluate side-chains 67 residues out of total 503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 475 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 40 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 53 optimal weight: 0.0040 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4934 Z= 0.176 Angle : 0.553 7.225 6728 Z= 0.280 Chirality : 0.040 0.164 782 Planarity : 0.005 0.042 824 Dihedral : 6.367 97.861 702 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.99 % Allowed : 12.92 % Favored : 85.09 % 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: 1.17 (0.35), residues: 613 helix: 1.40 (0.26), residues: 442 sheet: None (None), residues: 0 loop : -0.78 (0.48), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 487 HIS 0.002 0.001 HIS A 555 PHE 0.008 0.001 PHE A 534 TYR 0.019 0.001 TYR A 256 ARG 0.003 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.555 Fit side-chains REVERT: A 91 SER cc_start: 0.8509 (m) cc_final: 0.8249 (p) REVERT: A 131 LYS cc_start: 0.8259 (mtpt) cc_final: 0.8048 (mtmt) REVERT: A 150 TYR cc_start: 0.8298 (m-10) cc_final: 0.7579 (m-10) REVERT: A 216 MET cc_start: 0.8090 (ttp) cc_final: 0.7557 (ttp) REVERT: A 382 MET cc_start: 0.7846 (mmm) cc_final: 0.7459 (mmm) REVERT: A 412 ARG cc_start: 0.7075 (ttt180) cc_final: 0.5923 (tmt-80) REVERT: A 553 ARG cc_start: 0.7428 (mtp-110) cc_final: 0.6916 (ttp80) REVERT: A 569 GLU cc_start: 0.8296 (tp30) cc_final: 0.7729 (mp0) outliers start: 10 outliers final: 9 residues processed: 67 average time/residue: 0.2414 time to fit residues: 19.6508 Evaluate side-chains 68 residues out of total 503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 475 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4934 Z= 0.150 Angle : 0.531 7.196 6728 Z= 0.269 Chirality : 0.039 0.164 782 Planarity : 0.004 0.041 824 Dihedral : 6.259 97.880 702 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.39 % Allowed : 12.13 % Favored : 85.49 % 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: 1.37 (0.35), residues: 613 helix: 1.53 (0.26), residues: 441 sheet: None (None), residues: 0 loop : -0.64 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 289 HIS 0.002 0.000 HIS A 555 PHE 0.007 0.001 PHE A 534 TYR 0.019 0.001 TYR A 256 ARG 0.003 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.516 Fit side-chains REVERT: A 91 SER cc_start: 0.8570 (m) cc_final: 0.8280 (p) REVERT: A 131 LYS cc_start: 0.8242 (mtpt) cc_final: 0.8032 (mtmt) REVERT: A 150 TYR cc_start: 0.8310 (m-10) cc_final: 0.7613 (m-10) REVERT: A 216 MET cc_start: 0.8094 (ttp) cc_final: 0.7683 (ttp) REVERT: A 412 ARG cc_start: 0.7013 (ttt180) cc_final: 0.5912 (tmt-80) REVERT: A 553 ARG cc_start: 0.7398 (mtp-110) cc_final: 0.6884 (ttp80) REVERT: A 569 GLU cc_start: 0.8370 (tp30) cc_final: 0.7724 (mp0) outliers start: 12 outliers final: 8 residues processed: 71 average time/residue: 0.2178 time to fit residues: 19.0700 Evaluate side-chains 68 residues out of total 503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 475 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 0.0040 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4934 Z= 0.177 Angle : 0.548 7.191 6728 Z= 0.278 Chirality : 0.040 0.165 782 Planarity : 0.005 0.041 824 Dihedral : 6.266 98.261 702 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.58 % Allowed : 11.93 % Favored : 85.49 % 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: 1.25 (0.35), residues: 613 helix: 1.40 (0.25), residues: 445 sheet: None (None), residues: 0 loop : -0.62 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 487 HIS 0.002 0.001 HIS A 555 PHE 0.009 0.001 PHE A 534 TYR 0.018 0.001 TYR A 256 ARG 0.002 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.566 Fit side-chains REVERT: A 91 SER cc_start: 0.8587 (m) cc_final: 0.8289 (p) REVERT: A 131 LYS cc_start: 0.8211 (mtpt) cc_final: 0.8006 (mtmt) REVERT: A 150 TYR cc_start: 0.8320 (m-10) cc_final: 0.7614 (m-10) REVERT: A 198 MET cc_start: 0.7932 (mtt) cc_final: 0.7503 (mtt) REVERT: A 216 MET cc_start: 0.8113 (ttp) cc_final: 0.7690 (ttp) REVERT: A 382 MET cc_start: 0.7910 (mmm) cc_final: 0.7523 (mmm) REVERT: A 412 ARG cc_start: 0.7016 (ttt180) cc_final: 0.5920 (tmt-80) REVERT: A 569 GLU cc_start: 0.8386 (tp30) cc_final: 0.7790 (mp0) outliers start: 13 outliers final: 10 residues processed: 70 average time/residue: 0.2229 time to fit residues: 19.1898 Evaluate side-chains 71 residues out of total 503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 475 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 0.0070 chunk 56 optimal weight: 0.0770 chunk 51 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4934 Z= 0.143 Angle : 0.518 7.166 6728 Z= 0.262 Chirality : 0.039 0.175 782 Planarity : 0.004 0.040 824 Dihedral : 6.161 98.116 702 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.19 % Allowed : 13.52 % Favored : 85.29 % 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: 1.42 (0.35), residues: 613 helix: 1.56 (0.26), residues: 441 sheet: None (None), residues: 0 loop : -0.59 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 289 HIS 0.002 0.000 HIS A 555 PHE 0.008 0.001 PHE A 534 TYR 0.018 0.001 TYR A 256 ARG 0.002 0.000 ARG A 352 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.528 Fit side-chains REVERT: A 91 SER cc_start: 0.8546 (m) cc_final: 0.8280 (p) REVERT: A 150 TYR cc_start: 0.8314 (m-10) cc_final: 0.7626 (m-10) REVERT: A 198 MET cc_start: 0.7890 (mtt) cc_final: 0.7534 (mtt) REVERT: A 216 MET cc_start: 0.8101 (ttp) cc_final: 0.7658 (ttp) REVERT: A 382 MET cc_start: 0.7843 (mmm) cc_final: 0.7515 (mmm) REVERT: A 412 ARG cc_start: 0.7011 (ttt180) cc_final: 0.5926 (tmt-80) REVERT: A 553 ARG cc_start: 0.7404 (mtp-110) cc_final: 0.6889 (ttp80) outliers start: 6 outliers final: 6 residues processed: 67 average time/residue: 0.2296 time to fit residues: 18.8716 Evaluate side-chains 67 residues out of total 503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 505 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4934 Z= 0.164 Angle : 0.545 9.967 6728 Z= 0.272 Chirality : 0.039 0.176 782 Planarity : 0.004 0.040 824 Dihedral : 6.182 98.602 702 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.39 % Allowed : 13.92 % Favored : 84.69 % 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: 1.37 (0.35), residues: 613 helix: 1.49 (0.26), residues: 442 sheet: None (None), residues: 0 loop : -0.53 (0.50), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 487 HIS 0.002 0.000 HIS A 555 PHE 0.008 0.001 PHE A 534 TYR 0.017 0.001 TYR A 256 ARG 0.002 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.550 Fit side-chains REVERT: A 91 SER cc_start: 0.8554 (m) cc_final: 0.8275 (p) REVERT: A 150 TYR cc_start: 0.8318 (m-10) cc_final: 0.7618 (m-10) REVERT: A 198 MET cc_start: 0.7926 (mtt) cc_final: 0.7506 (mtt) REVERT: A 216 MET cc_start: 0.8089 (ttp) cc_final: 0.7654 (ttp) REVERT: A 412 ARG cc_start: 0.7013 (ttt180) cc_final: 0.5914 (tmt-80) REVERT: A 569 GLU cc_start: 0.8083 (tp30) cc_final: 0.7359 (mp0) outliers start: 7 outliers final: 7 residues processed: 68 average time/residue: 0.2248 time to fit residues: 18.7531 Evaluate side-chains 69 residues out of total 503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 475 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4934 Z= 0.148 Angle : 0.538 8.331 6728 Z= 0.269 Chirality : 0.039 0.180 782 Planarity : 0.004 0.040 824 Dihedral : 6.139 98.569 702 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.59 % Allowed : 13.92 % Favored : 84.49 % 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: 1.45 (0.35), residues: 613 helix: 1.57 (0.26), residues: 441 sheet: None (None), residues: 0 loop : -0.53 (0.50), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 289 HIS 0.002 0.000 HIS A 555 PHE 0.008 0.001 PHE A 534 TYR 0.018 0.001 TYR A 256 ARG 0.002 0.000 ARG A 352 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.479 Fit side-chains REVERT: A 91 SER cc_start: 0.8533 (m) cc_final: 0.8274 (p) REVERT: A 150 TYR cc_start: 0.8317 (m-10) cc_final: 0.7626 (m-10) REVERT: A 198 MET cc_start: 0.7896 (mtt) cc_final: 0.7526 (mtt) REVERT: A 216 MET cc_start: 0.8075 (ttp) cc_final: 0.7637 (ttp) REVERT: A 412 ARG cc_start: 0.7029 (ttt180) cc_final: 0.5916 (tmt-80) REVERT: A 553 ARG cc_start: 0.7406 (mtp-110) cc_final: 0.6896 (ttp80) REVERT: A 569 GLU cc_start: 0.8051 (tp30) cc_final: 0.7343 (mp0) outliers start: 8 outliers final: 8 residues processed: 69 average time/residue: 0.2212 time to fit residues: 18.8344 Evaluate side-chains 69 residues out of total 503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 505 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 0.0000 chunk 49 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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 = 0.3311 r_free = 0.3311 target = 0.126590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.106858 restraints weight = 5119.464| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.22 r_work: 0.2976 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4934 Z= 0.140 Angle : 0.521 7.162 6728 Z= 0.263 Chirality : 0.039 0.181 782 Planarity : 0.004 0.040 824 Dihedral : 6.090 98.683 702 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.19 % Allowed : 14.51 % Favored : 84.29 % 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: 1.54 (0.35), residues: 613 helix: 1.63 (0.26), residues: 441 sheet: None (None), residues: 0 loop : -0.52 (0.50), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 289 HIS 0.002 0.000 HIS A 555 PHE 0.007 0.001 PHE A 534 TYR 0.017 0.001 TYR A 256 ARG 0.003 0.000 ARG A 352 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1368.07 seconds wall clock time: 25 minutes 22.34 seconds (1522.34 seconds total)