Starting phenix.real_space_refine on Mon Sep 23 23:00:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtn_24684/09_2024/7rtn_24684.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtn_24684/09_2024/7rtn_24684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtn_24684/09_2024/7rtn_24684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtn_24684/09_2024/7rtn_24684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtn_24684/09_2024/7rtn_24684.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtn_24684/09_2024/7rtn_24684.cif" } resolution = 3.4 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= 0.002 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 3792 2.51 5 N 1098 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6018 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2006 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2006 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2006 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Time building chain proxies: 4.43, per 1000 atoms: 0.74 Number of scatterers: 6018 At special positions: 0 Unit cell: (104.72, 104.72, 111.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 1116 8.00 N 1098 7.00 C 3792 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 788.9 milliseconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1512 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 6 sheets defined 56.7% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 64 through 80 removed outlier: 3.967A pdb=" N SER A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 135 removed outlier: 3.719A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 340 Proline residue: A 326 - end of helix Processing helix chain 'A' and resid 346 through 353 removed outlier: 3.982A pdb=" N VAL A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET A 352 " --> pdb=" O PRO A 348 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 438 Processing helix chain 'A' and resid 446 through 455 removed outlier: 3.911A pdb=" N ARG A 452 " --> pdb=" O ARG A 448 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 483 Processing helix chain 'A' and resid 484 through 491 Processing helix chain 'A' and resid 494 through 508 Processing helix chain 'B' and resid 65 through 79 removed outlier: 4.009A pdb=" N LYS B 70 " --> pdb=" O GLY B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 135 removed outlier: 3.531A pdb=" N ARG B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN B 135 " --> pdb=" O TYR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 340 removed outlier: 3.970A pdb=" N GLY B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.755A pdb=" N PHE B 354 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS B 355 " --> pdb=" O MET B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 438 removed outlier: 3.550A pdb=" N SER B 438 " --> pdb=" O ASN B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 455 removed outlier: 3.953A pdb=" N THR B 455 " --> pdb=" O VAL B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 483 Processing helix chain 'B' and resid 483 through 491 Processing helix chain 'B' and resid 494 through 509 Processing helix chain 'C' and resid 65 through 79 Processing helix chain 'C' and resid 89 through 135 removed outlier: 3.501A pdb=" N ARG C 93 " --> pdb=" O SER C 89 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ASN C 135 " --> pdb=" O TYR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 340 Proline residue: C 326 - end of helix removed outlier: 4.037A pdb=" N GLY C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 424 through 438 Processing helix chain 'C' and resid 445 through 454 Processing helix chain 'C' and resid 469 through 483 removed outlier: 3.843A pdb=" N VAL C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 491 removed outlier: 3.838A pdb=" N HIS C 489 " --> pdb=" O GLU C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 509 removed outlier: 3.586A pdb=" N ARG C 500 " --> pdb=" O HIS C 496 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 401 through 406 removed outlier: 5.696A pdb=" N ILE A 364 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER A 463 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL A 366 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 410 through 414 Processing sheet with id=AA3, first strand: chain 'B' and resid 401 through 408 removed outlier: 6.666A pdb=" N ILE B 364 " --> pdb=" O SER B 463 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER B 463 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL B 366 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 410 through 414 Processing sheet with id=AA5, first strand: chain 'C' and resid 401 through 406 removed outlier: 6.421A pdb=" N ILE C 364 " --> pdb=" O SER C 463 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER C 463 " --> pdb=" O ILE C 364 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL C 366 " --> pdb=" O LEU C 461 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 410 through 414 408 hydrogen bonds defined for protein. 1176 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: 1.50 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2085 1.34 - 1.46: 1019 1.46 - 1.58: 3022 1.58 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 6144 Sorted by residual: bond pdb=" CG LYS B 98 " pdb=" CD LYS B 98 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.30e+00 bond pdb=" CA GLN C 444 " pdb=" CB GLN C 444 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.69e-02 3.50e+03 1.08e+00 bond pdb=" CB GLU C 82 " pdb=" CG GLU C 82 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.31e-01 bond pdb=" CG GLU C 82 " pdb=" CD GLU C 82 " ideal model delta sigma weight residual 1.516 1.493 0.023 2.50e-02 1.60e+03 8.25e-01 bond pdb=" N GLN C 444 " pdb=" CA GLN C 444 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 7.98e-01 ... (remaining 6139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 8200 2.00 - 3.99: 123 3.99 - 5.99: 11 5.99 - 7.99: 7 7.99 - 9.99: 2 Bond angle restraints: 8343 Sorted by residual: angle pdb=" C THR C 443 " pdb=" N GLN C 444 " pdb=" CA GLN C 444 " ideal model delta sigma weight residual 121.54 129.05 -7.51 1.91e+00 2.74e-01 1.55e+01 angle pdb=" C THR B 443 " pdb=" N GLN B 444 " pdb=" CA GLN B 444 " ideal model delta sigma weight residual 121.54 128.76 -7.22 1.91e+00 2.74e-01 1.43e+01 angle pdb=" C HIS C 384 " pdb=" N HIS C 385 " pdb=" CA HIS C 385 " ideal model delta sigma weight residual 121.54 128.01 -6.47 1.91e+00 2.74e-01 1.15e+01 angle pdb=" CA LEU B 414 " pdb=" CB LEU B 414 " pdb=" CG LEU B 414 " ideal model delta sigma weight residual 116.30 126.29 -9.99 3.50e+00 8.16e-02 8.14e+00 angle pdb=" CA GLN C 444 " pdb=" CB GLN C 444 " pdb=" CG GLN C 444 " ideal model delta sigma weight residual 114.10 119.53 -5.43 2.00e+00 2.50e-01 7.36e+00 ... (remaining 8338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 3244 17.84 - 35.68: 311 35.68 - 53.52: 55 53.52 - 71.36: 10 71.36 - 89.19: 4 Dihedral angle restraints: 3624 sinusoidal: 1284 harmonic: 2340 Sorted by residual: dihedral pdb=" CA TYR C 65 " pdb=" C TYR C 65 " pdb=" N GLY C 66 " pdb=" CA GLY C 66 " ideal model delta harmonic sigma weight residual 180.00 -158.17 -21.83 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA HIS B 385 " pdb=" C HIS B 385 " pdb=" N HIS B 386 " pdb=" CA HIS B 386 " ideal model delta harmonic sigma weight residual 180.00 158.93 21.07 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA HIS A 385 " pdb=" C HIS A 385 " pdb=" N HIS A 386 " pdb=" CA HIS A 386 " ideal model delta harmonic sigma weight residual 180.00 163.30 16.70 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 3621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 584 0.035 - 0.070: 249 0.070 - 0.105: 70 0.105 - 0.139: 25 0.139 - 0.174: 2 Chirality restraints: 930 Sorted by residual: chirality pdb=" CB ILE B 399 " pdb=" CA ILE B 399 " pdb=" CG1 ILE B 399 " pdb=" CG2 ILE B 399 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA PRO A 370 " pdb=" N PRO A 370 " pdb=" C PRO A 370 " pdb=" CB PRO A 370 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CG LEU C 433 " pdb=" CB LEU C 433 " pdb=" CD1 LEU C 433 " pdb=" CD2 LEU C 433 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 927 not shown) Planarity restraints: 1107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 89 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO C 90 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 90 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 90 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 89 " 0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO A 90 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 90 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 90 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 378 " -0.013 2.00e-02 2.50e+03 9.35e-03 1.53e+00 pdb=" CG PHE C 378 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE C 378 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE C 378 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 378 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 378 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 378 " -0.005 2.00e-02 2.50e+03 ... (remaining 1104 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1748 2.82 - 3.34: 5705 3.34 - 3.86: 9613 3.86 - 4.38: 10615 4.38 - 4.90: 18932 Nonbonded interactions: 46613 Sorted by model distance: nonbonded pdb=" O ALA B 369 " pdb=" OG SER B 373 " model vdw 2.298 3.040 nonbonded pdb=" O HIS A 384 " pdb=" ND1 HIS A 385 " model vdw 2.311 3.120 nonbonded pdb=" O HIS B 384 " pdb=" ND1 HIS B 385 " model vdw 2.317 3.120 nonbonded pdb=" O SER C 89 " pdb=" OG SER C 89 " model vdw 2.351 3.040 nonbonded pdb=" OD2 ASP C 86 " pdb=" NH2 ARG C 499 " model vdw 2.353 3.120 ... (remaining 46608 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.820 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.300 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 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 : 0.004 0.045 6144 Z= 0.237 Angle : 0.631 9.986 8343 Z= 0.333 Chirality : 0.044 0.174 930 Planarity : 0.004 0.036 1107 Dihedral : 14.578 89.195 2112 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: 0.60 (0.31), residues: 798 helix: 1.96 (0.25), residues: 423 sheet: -0.01 (0.44), residues: 139 loop : -2.36 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 371 HIS 0.008 0.001 HIS B 489 PHE 0.020 0.002 PHE C 378 TYR 0.015 0.001 TYR A 367 ARG 0.003 0.000 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.637 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1650 time to fit residues: 25.2523 Evaluate side-chains 87 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 20.0000 chunk 61 optimal weight: 0.4980 chunk 34 optimal weight: 0.0670 chunk 20 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 overall best weight: 3.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6144 Z= 0.168 Angle : 0.546 8.375 8343 Z= 0.289 Chirality : 0.041 0.152 930 Planarity : 0.003 0.031 1107 Dihedral : 4.171 20.613 870 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.62 % Allowed : 10.81 % Favored : 87.57 % 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: 0.88 (0.31), residues: 798 helix: 2.22 (0.25), residues: 438 sheet: 0.15 (0.46), residues: 136 loop : -2.63 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 371 HIS 0.005 0.001 HIS B 385 PHE 0.019 0.002 PHE C 378 TYR 0.011 0.001 TYR A 367 ARG 0.002 0.000 ARG C 500 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.630 Fit side-chains REVERT: A 400 ASP cc_start: 0.6213 (t0) cc_final: 0.5995 (t0) REVERT: A 438 SER cc_start: 0.7629 (m) cc_final: 0.7427 (p) REVERT: B 482 TYR cc_start: 0.7644 (OUTLIER) cc_final: 0.7272 (p90) outliers start: 9 outliers final: 6 residues processed: 94 average time/residue: 0.1510 time to fit residues: 19.8071 Evaluate side-chains 91 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 20.0000 chunk 22 optimal weight: 0.0470 chunk 61 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 73 optimal weight: 40.0000 chunk 79 optimal weight: 0.0670 chunk 65 optimal weight: 30.0000 chunk 25 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 overall best weight: 4.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6144 Z= 0.180 Angle : 0.531 8.272 8343 Z= 0.281 Chirality : 0.041 0.141 930 Planarity : 0.003 0.033 1107 Dihedral : 4.131 20.783 870 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.34 % Allowed : 11.35 % Favored : 86.31 % 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 (0.31), residues: 798 helix: 2.37 (0.25), residues: 435 sheet: 0.17 (0.46), residues: 136 loop : -2.55 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 371 HIS 0.006 0.001 HIS A 385 PHE 0.018 0.002 PHE A 378 TYR 0.010 0.001 TYR A 367 ARG 0.002 0.000 ARG C 500 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.710 Fit side-chains REVERT: B 482 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.7330 (p90) outliers start: 13 outliers final: 9 residues processed: 95 average time/residue: 0.1525 time to fit residues: 20.0091 Evaluate side-chains 93 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS C 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6144 Z= 0.243 Angle : 0.566 8.297 8343 Z= 0.299 Chirality : 0.042 0.140 930 Planarity : 0.004 0.033 1107 Dihedral : 4.373 21.413 870 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.78 % Allowed : 12.43 % Favored : 83.78 % 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: 0.92 (0.31), residues: 798 helix: 2.27 (0.25), residues: 434 sheet: 0.11 (0.45), residues: 136 loop : -2.52 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 371 HIS 0.009 0.001 HIS B 385 PHE 0.019 0.002 PHE A 378 TYR 0.012 0.001 TYR A 367 ARG 0.003 0.000 ARG C 500 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 0.706 Fit side-chains REVERT: B 482 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.7340 (p90) REVERT: B 489 HIS cc_start: 0.8361 (OUTLIER) cc_final: 0.8092 (m170) REVERT: C 103 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6593 (tm-30) outliers start: 21 outliers final: 13 residues processed: 102 average time/residue: 0.1345 time to fit residues: 19.5721 Evaluate side-chains 95 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 8.9990 chunk 58 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 39 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6144 Z= 0.223 Angle : 0.560 8.331 8343 Z= 0.296 Chirality : 0.041 0.148 930 Planarity : 0.003 0.034 1107 Dihedral : 4.308 21.016 870 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.42 % Allowed : 14.05 % Favored : 82.52 % 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: 0.99 (0.31), residues: 798 helix: 2.31 (0.25), residues: 432 sheet: 0.17 (0.46), residues: 133 loop : -2.38 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 371 HIS 0.009 0.001 HIS B 385 PHE 0.019 0.002 PHE A 378 TYR 0.011 0.001 TYR A 367 ARG 0.002 0.000 ARG C 500 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 0.708 Fit side-chains REVERT: B 482 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.7248 (p90) REVERT: B 489 HIS cc_start: 0.8323 (OUTLIER) cc_final: 0.7962 (m170) REVERT: C 103 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6553 (tm-30) outliers start: 19 outliers final: 14 residues processed: 95 average time/residue: 0.1427 time to fit residues: 19.2094 Evaluate side-chains 99 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 75 optimal weight: 0.2980 chunk 8 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS C 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6144 Z= 0.180 Angle : 0.537 8.245 8343 Z= 0.283 Chirality : 0.040 0.137 930 Planarity : 0.003 0.036 1107 Dihedral : 4.141 20.514 870 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.60 % Allowed : 14.41 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.31), residues: 798 helix: 2.43 (0.25), residues: 432 sheet: 0.42 (0.47), residues: 130 loop : -2.38 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 371 HIS 0.009 0.001 HIS B 385 PHE 0.018 0.002 PHE C 378 TYR 0.011 0.001 TYR A 367 ARG 0.003 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 0.738 Fit side-chains REVERT: B 105 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6884 (tm-30) REVERT: B 482 TYR cc_start: 0.7733 (OUTLIER) cc_final: 0.7230 (p90) REVERT: B 489 HIS cc_start: 0.8218 (OUTLIER) cc_final: 0.7805 (m170) REVERT: C 103 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6607 (tm-30) outliers start: 20 outliers final: 15 residues processed: 101 average time/residue: 0.1487 time to fit residues: 21.2689 Evaluate side-chains 100 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 chunk 43 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 23 optimal weight: 30.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN A 365 HIS B 457 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6144 Z= 0.177 Angle : 0.537 8.138 8343 Z= 0.281 Chirality : 0.040 0.130 930 Planarity : 0.003 0.036 1107 Dihedral : 4.119 20.381 870 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.14 % Allowed : 14.77 % Favored : 81.08 % 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: 1.25 (0.31), residues: 798 helix: 2.50 (0.25), residues: 432 sheet: 0.48 (0.47), residues: 130 loop : -2.33 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 371 HIS 0.009 0.001 HIS B 385 PHE 0.018 0.002 PHE C 378 TYR 0.017 0.001 TYR A 466 ARG 0.002 0.000 ARG C 500 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 82 time to evaluate : 0.693 Fit side-chains REVERT: A 115 TYR cc_start: 0.3157 (OUTLIER) cc_final: 0.2795 (t80) REVERT: B 105 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6868 (tm-30) REVERT: B 482 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.6910 (p90) REVERT: B 489 HIS cc_start: 0.8225 (OUTLIER) cc_final: 0.7755 (m170) REVERT: C 103 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6600 (tm-30) outliers start: 23 outliers final: 17 residues processed: 100 average time/residue: 0.1344 time to fit residues: 19.0763 Evaluate side-chains 103 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 81 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 7 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN B 457 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6144 Z= 0.183 Angle : 0.537 8.093 8343 Z= 0.282 Chirality : 0.040 0.137 930 Planarity : 0.003 0.036 1107 Dihedral : 4.133 20.399 870 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.14 % Allowed : 15.14 % Favored : 80.72 % 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: 1.29 (0.31), residues: 798 helix: 2.52 (0.25), residues: 432 sheet: 0.72 (0.48), residues: 124 loop : -2.38 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 371 HIS 0.009 0.001 HIS B 385 PHE 0.017 0.002 PHE C 378 TYR 0.013 0.001 TYR A 466 ARG 0.002 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 83 time to evaluate : 0.723 Fit side-chains REVERT: A 115 TYR cc_start: 0.2976 (OUTLIER) cc_final: 0.2701 (t80) REVERT: B 105 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6890 (tm-30) REVERT: B 482 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.6908 (p90) REVERT: B 489 HIS cc_start: 0.8235 (OUTLIER) cc_final: 0.7785 (m170) REVERT: C 103 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6601 (tm-30) outliers start: 23 outliers final: 17 residues processed: 101 average time/residue: 0.1527 time to fit residues: 21.8955 Evaluate side-chains 101 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 68 optimal weight: 0.0010 chunk 72 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 overall best weight: 2.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN B 457 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6144 Z= 0.143 Angle : 0.521 8.095 8343 Z= 0.271 Chirality : 0.040 0.142 930 Planarity : 0.003 0.036 1107 Dihedral : 3.918 19.737 870 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.78 % Allowed : 16.04 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.31), residues: 798 helix: 2.63 (0.25), residues: 432 sheet: 0.81 (0.48), residues: 124 loop : -2.40 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 371 HIS 0.008 0.001 HIS B 385 PHE 0.019 0.002 PHE C 392 TYR 0.012 0.001 TYR A 466 ARG 0.002 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 0.704 Fit side-chains REVERT: A 115 TYR cc_start: 0.2921 (OUTLIER) cc_final: 0.2656 (t80) REVERT: A 385 HIS cc_start: 0.7169 (OUTLIER) cc_final: 0.6263 (p-80) REVERT: B 105 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6856 (tm-30) REVERT: B 482 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.6840 (p90) REVERT: B 489 HIS cc_start: 0.8033 (OUTLIER) cc_final: 0.7562 (m-70) REVERT: C 103 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6549 (tm-30) outliers start: 21 outliers final: 13 residues processed: 102 average time/residue: 0.1468 time to fit residues: 21.3132 Evaluate side-chains 101 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 64 optimal weight: 30.0000 chunk 6 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 39 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN A 412 HIS B 457 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6144 Z= 0.190 Angle : 0.542 8.057 8343 Z= 0.285 Chirality : 0.041 0.150 930 Planarity : 0.003 0.038 1107 Dihedral : 4.109 21.449 870 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.24 % Allowed : 17.48 % Favored : 79.28 % 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 (0.31), residues: 798 helix: 2.60 (0.25), residues: 433 sheet: 0.79 (0.48), residues: 124 loop : -2.41 (0.35), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 371 HIS 0.009 0.001 HIS B 385 PHE 0.018 0.002 PHE C 378 TYR 0.012 0.001 TYR A 466 ARG 0.002 0.000 ARG C 500 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.690 Fit side-chains REVERT: A 115 TYR cc_start: 0.2983 (OUTLIER) cc_final: 0.2702 (t80) REVERT: A 385 HIS cc_start: 0.7296 (OUTLIER) cc_final: 0.6379 (p-80) REVERT: B 105 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6875 (tm-30) REVERT: B 482 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.6903 (p90) REVERT: B 489 HIS cc_start: 0.8222 (OUTLIER) cc_final: 0.7757 (m170) REVERT: C 103 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6582 (tm-30) outliers start: 18 outliers final: 12 residues processed: 98 average time/residue: 0.1374 time to fit residues: 19.0249 Evaluate side-chains 96 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 30.0000 chunk 64 optimal weight: 30.0000 chunk 26 optimal weight: 8.9990 chunk 66 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 11 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS B 457 HIS ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.172835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.146499 restraints weight = 9458.088| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.21 r_work: 0.3516 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6144 Z= 0.221 Angle : 0.558 8.069 8343 Z= 0.294 Chirality : 0.041 0.157 930 Planarity : 0.003 0.038 1107 Dihedral : 4.282 23.688 870 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.42 % Allowed : 17.30 % Favored : 79.28 % 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: 1.29 (0.31), residues: 798 helix: 2.51 (0.25), residues: 433 sheet: 0.74 (0.48), residues: 124 loop : -2.38 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 371 HIS 0.009 0.001 HIS B 385 PHE 0.018 0.002 PHE C 378 TYR 0.012 0.001 TYR A 466 ARG 0.002 0.000 ARG C 500 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1442.35 seconds wall clock time: 26 minutes 30.00 seconds (1590.00 seconds total)