Starting phenix.real_space_refine on Sun Mar 10 20:38:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dad_27270/03_2024/8dad_27270.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dad_27270/03_2024/8dad_27270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dad_27270/03_2024/8dad_27270.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dad_27270/03_2024/8dad_27270.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dad_27270/03_2024/8dad_27270.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dad_27270/03_2024/8dad_27270.pdb" } resolution = 3.85 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= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1656 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 2068 2.51 5 N 558 2.21 5 O 610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L GLU 106": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3255 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1428 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 55 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.33, per 1000 atoms: 0.72 Number of scatterers: 3255 At special positions: 0 Unit cell: (62.83, 64.89, 101.97, 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 19 16.00 O 610 8.00 N 558 7.00 C 2068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 1 " - " ASN B 343 " Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 606.3 milliseconds 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 8 sheets defined 12.0% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.898A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.194A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.215A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.585A pdb=" N MET H 112 " --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.638A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'B' and resid 473 through 474 121 hydrogen bonds defined for protein. 285 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: 0.84 Time building geometry restraints manager: 1.42 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: 1052 1.34 - 1.46: 889 1.46 - 1.58: 1371 1.58 - 1.70: 0 1.70 - 1.83: 24 Bond restraints: 3336 Sorted by residual: bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.94e+00 bond pdb=" C1 NAG J 1 " pdb=" C2 NAG J 1 " ideal model delta sigma weight residual 1.532 1.506 0.026 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C5 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.413 1.439 -0.026 2.00e-02 2.50e+03 1.72e+00 ... (remaining 3331 not shown) Histogram of bond angle deviations from ideal: 100.17 - 106.93: 105 106.93 - 113.69: 1725 113.69 - 120.45: 1239 120.45 - 127.21: 1441 127.21 - 133.98: 34 Bond angle restraints: 4544 Sorted by residual: angle pdb=" N CYS B 391 " pdb=" CA CYS B 391 " pdb=" C CYS B 391 " ideal model delta sigma weight residual 107.69 120.41 -12.72 2.01e+00 2.48e-01 4.00e+01 angle pdb=" N LEU B 390 " pdb=" CA LEU B 390 " pdb=" C LEU B 390 " ideal model delta sigma weight residual 109.76 115.86 -6.10 1.59e+00 3.96e-01 1.47e+01 angle pdb=" CA CYS B 391 " pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " ideal model delta sigma weight residual 114.40 122.98 -8.58 2.30e+00 1.89e-01 1.39e+01 angle pdb=" CB MET H 118 " pdb=" CG MET H 118 " pdb=" SD MET H 118 " ideal model delta sigma weight residual 112.70 123.10 -10.40 3.00e+00 1.11e-01 1.20e+01 angle pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " ideal model delta sigma weight residual 114.40 121.52 -7.12 2.30e+00 1.89e-01 9.57e+00 ... (remaining 4539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.03: 1767 20.03 - 40.07: 195 40.07 - 60.10: 38 60.10 - 80.13: 7 80.13 - 100.17: 10 Dihedral angle restraints: 2017 sinusoidal: 791 harmonic: 1226 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -166.15 80.15 1 1.00e+01 1.00e-02 7.96e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 19.42 73.58 1 1.00e+01 1.00e-02 6.89e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 164.39 -71.39 1 1.00e+01 1.00e-02 6.54e+01 ... (remaining 2014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 477 0.106 - 0.212: 23 0.212 - 0.318: 0 0.318 - 0.424: 0 0.424 - 0.529: 1 Chirality restraints: 501 Sorted by residual: chirality pdb=" CA CYS B 391 " pdb=" N CYS B 391 " pdb=" C CYS B 391 " pdb=" CB CYS B 391 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.00e+00 chirality pdb=" C4 NAG J 1 " pdb=" C3 NAG J 1 " pdb=" C5 NAG J 1 " pdb=" O4 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.34 -0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 7.44e-01 ... (remaining 498 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 36 " -0.012 2.00e-02 2.50e+03 1.85e-02 8.60e+00 pdb=" CG TRP L 36 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP L 36 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP L 36 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP L 36 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP L 36 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP L 36 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 36 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 36 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP L 36 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY H 8 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.61e+00 pdb=" N PRO H 9 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO H 9 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 9 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 526 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO B 527 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " -0.022 5.00e-02 4.00e+02 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 631 2.77 - 3.30: 3114 3.30 - 3.84: 5612 3.84 - 4.37: 6247 4.37 - 4.90: 10905 Nonbonded interactions: 26509 Sorted by model distance: nonbonded pdb=" N GLU H 66 " pdb=" OE1 GLU H 66 " model vdw 2.238 2.520 nonbonded pdb=" OH TYR L 37 " pdb=" OE1 GLN L 90 " model vdw 2.287 2.440 nonbonded pdb=" O THR H 104 " pdb=" OH TYR B 473 " model vdw 2.293 2.440 nonbonded pdb=" OD2 ASP H 108 " pdb=" NH1 ARG L 54 " model vdw 2.310 2.520 nonbonded pdb=" N GLN H 65 " pdb=" OE1 GLN H 65 " model vdw 2.317 2.520 ... (remaining 26504 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'J' } 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 group one per residue 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 6.750 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.910 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 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 0.033 3336 Z= 0.279 Angle : 0.832 12.716 4544 Z= 0.428 Chirality : 0.054 0.529 501 Planarity : 0.006 0.054 588 Dihedral : 17.766 100.167 1216 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.63 % Allowed : 26.98 % Favored : 72.38 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 9.52 % 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: -0.96 (0.42), residues: 418 helix: -2.01 (0.96), residues: 33 sheet: -0.55 (0.44), residues: 146 loop : -0.37 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP L 36 PHE 0.013 0.002 PHE H 27 TYR 0.009 0.001 TYR L 92 ARG 0.004 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 424 LYS cc_start: 0.8407 (ttpp) cc_final: 0.8126 (ttpp) outliers start: 2 outliers final: 1 residues processed: 79 average time/residue: 0.2095 time to fit residues: 19.2031 Evaluate side-chains 72 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.0270 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3336 Z= 0.233 Angle : 0.661 7.423 4544 Z= 0.333 Chirality : 0.046 0.157 501 Planarity : 0.005 0.050 588 Dihedral : 10.923 75.819 556 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.49 % Allowed : 24.76 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.97 (0.42), residues: 418 helix: -2.01 (0.98), residues: 34 sheet: -0.75 (0.41), residues: 153 loop : -0.19 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP L 36 PHE 0.034 0.002 PHE B 392 TYR 0.010 0.001 TYR L 92 ARG 0.003 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 112 MET cc_start: 0.7696 (mpp) cc_final: 0.6541 (mpp) REVERT: B 424 LYS cc_start: 0.8402 (ttpp) cc_final: 0.8144 (ttpp) outliers start: 11 outliers final: 7 residues processed: 82 average time/residue: 0.1921 time to fit residues: 18.4841 Evaluate side-chains 77 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3336 Z= 0.214 Angle : 0.673 9.235 4544 Z= 0.334 Chirality : 0.046 0.176 501 Planarity : 0.005 0.047 588 Dihedral : 9.833 66.790 556 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 6.67 % Allowed : 21.90 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.87 (0.42), residues: 418 helix: -2.32 (0.90), residues: 34 sheet: -0.66 (0.42), residues: 146 loop : -0.11 (0.43), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 36 PHE 0.027 0.002 PHE B 392 TYR 0.010 0.001 TYR L 92 ARG 0.005 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 47 TRP cc_start: 0.7993 (t60) cc_final: 0.7728 (t60) REVERT: L 11 LEU cc_start: 0.8168 (mm) cc_final: 0.7849 (mm) REVERT: L 17 GLU cc_start: 0.7444 (pm20) cc_final: 0.6754 (pm20) REVERT: L 80 GLU cc_start: 0.7289 (tt0) cc_final: 0.7039 (tt0) outliers start: 21 outliers final: 11 residues processed: 91 average time/residue: 0.1942 time to fit residues: 20.8006 Evaluate side-chains 79 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain B residue 351 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 0.0770 chunk 33 optimal weight: 10.0000 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3336 Z= 0.279 Angle : 0.660 7.504 4544 Z= 0.332 Chirality : 0.046 0.156 501 Planarity : 0.007 0.124 588 Dihedral : 9.012 59.324 556 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 6.35 % Allowed : 23.17 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.42), residues: 418 helix: -2.36 (0.89), residues: 33 sheet: -0.88 (0.41), residues: 153 loop : -0.12 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 36 PHE 0.023 0.002 PHE B 392 TYR 0.010 0.001 TYR B 453 ARG 0.005 0.001 ARG L 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 75 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 47 TRP cc_start: 0.8117 (t60) cc_final: 0.7713 (t60) REVERT: H 112 MET cc_start: 0.7794 (mpp) cc_final: 0.7270 (mpp) REVERT: L 11 LEU cc_start: 0.8143 (mm) cc_final: 0.7851 (mm) REVERT: L 17 GLU cc_start: 0.7578 (pm20) cc_final: 0.6839 (pm20) outliers start: 20 outliers final: 17 residues processed: 86 average time/residue: 0.1819 time to fit residues: 18.5574 Evaluate side-chains 87 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.0870 chunk 33 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3336 Z= 0.237 Angle : 0.684 7.917 4544 Z= 0.337 Chirality : 0.045 0.132 501 Planarity : 0.006 0.082 588 Dihedral : 8.362 53.537 556 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.71 % Allowed : 23.49 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.90 (0.42), residues: 418 helix: -2.36 (0.88), residues: 33 sheet: -0.83 (0.41), residues: 152 loop : 0.01 (0.44), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 36 PHE 0.022 0.002 PHE H 29 TYR 0.011 0.001 TYR L 92 ARG 0.008 0.001 ARG L 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 47 TRP cc_start: 0.8135 (t60) cc_final: 0.7728 (t60) REVERT: H 112 MET cc_start: 0.7841 (mpp) cc_final: 0.7346 (mpp) REVERT: L 17 GLU cc_start: 0.7530 (pm20) cc_final: 0.6807 (pm20) outliers start: 18 outliers final: 16 residues processed: 87 average time/residue: 0.1963 time to fit residues: 19.9792 Evaluate side-chains 89 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3336 Z= 0.209 Angle : 0.659 7.836 4544 Z= 0.324 Chirality : 0.046 0.149 501 Planarity : 0.005 0.061 588 Dihedral : 7.405 46.058 556 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.40 % Allowed : 24.76 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -1.04 (0.42), residues: 418 helix: -2.43 (0.85), residues: 33 sheet: -0.90 (0.40), residues: 156 loop : -0.09 (0.44), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 36 PHE 0.028 0.002 PHE B 486 TYR 0.017 0.001 TYR H 80 ARG 0.005 0.000 ARG L 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.7079 (pm20) cc_final: 0.6637 (pm20) REVERT: H 47 TRP cc_start: 0.8194 (t60) cc_final: 0.7724 (t60) REVERT: H 112 MET cc_start: 0.7830 (mpp) cc_final: 0.7300 (mpp) REVERT: L 17 GLU cc_start: 0.7432 (pm20) cc_final: 0.6781 (pm20) REVERT: L 37 TYR cc_start: 0.8314 (m-80) cc_final: 0.8056 (m-80) REVERT: L 93 ARG cc_start: 0.7556 (tpp-160) cc_final: 0.7030 (tpm170) outliers start: 17 outliers final: 15 residues processed: 87 average time/residue: 0.1818 time to fit residues: 18.7344 Evaluate side-chains 85 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3336 Z= 0.208 Angle : 0.671 9.365 4544 Z= 0.328 Chirality : 0.046 0.189 501 Planarity : 0.008 0.163 588 Dihedral : 6.867 41.276 556 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 6.03 % Allowed : 25.08 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -1.09 (0.42), residues: 418 helix: -2.56 (0.83), residues: 33 sheet: -0.90 (0.40), residues: 158 loop : -0.13 (0.44), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP L 36 PHE 0.040 0.002 PHE B 486 TYR 0.021 0.001 TYR L 92 ARG 0.011 0.001 ARG L 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 47 TRP cc_start: 0.8213 (t60) cc_final: 0.7732 (t60) REVERT: H 112 MET cc_start: 0.7810 (mpp) cc_final: 0.7295 (mpp) REVERT: L 17 GLU cc_start: 0.7487 (pm20) cc_final: 0.6883 (pm20) REVERT: L 37 TYR cc_start: 0.8302 (m-80) cc_final: 0.8041 (m-80) REVERT: L 93 ARG cc_start: 0.7666 (tpp-160) cc_final: 0.7169 (tpm170) outliers start: 19 outliers final: 18 residues processed: 85 average time/residue: 0.1764 time to fit residues: 17.8357 Evaluate side-chains 90 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3336 Z= 0.277 Angle : 0.684 6.017 4544 Z= 0.341 Chirality : 0.046 0.183 501 Planarity : 0.007 0.122 588 Dihedral : 6.262 36.865 555 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 6.67 % Allowed : 24.44 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 (0.41), residues: 418 helix: -2.42 (0.86), residues: 33 sheet: -1.06 (0.39), residues: 158 loop : -0.13 (0.44), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 36 PHE 0.031 0.002 PHE B 486 TYR 0.017 0.001 TYR L 92 ARG 0.008 0.001 ARG L 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.7097 (pm20) cc_final: 0.6848 (pm20) REVERT: H 47 TRP cc_start: 0.8235 (t60) cc_final: 0.7761 (t60) REVERT: H 112 MET cc_start: 0.7852 (mpp) cc_final: 0.7324 (mpp) REVERT: L 17 GLU cc_start: 0.7549 (pm20) cc_final: 0.6857 (pm20) REVERT: L 37 TYR cc_start: 0.8338 (m-80) cc_final: 0.8074 (m-80) REVERT: L 93 ARG cc_start: 0.7746 (tpp-160) cc_final: 0.7243 (tpm170) REVERT: L 101 GLN cc_start: 0.8156 (mp10) cc_final: 0.7934 (mp10) outliers start: 21 outliers final: 20 residues processed: 86 average time/residue: 0.1824 time to fit residues: 18.7378 Evaluate side-chains 93 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3336 Z= 0.313 Angle : 0.702 6.439 4544 Z= 0.355 Chirality : 0.047 0.168 501 Planarity : 0.006 0.097 588 Dihedral : 6.060 32.823 555 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 7.62 % Allowed : 25.08 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.41), residues: 418 helix: -2.44 (0.86), residues: 33 sheet: -0.91 (0.39), residues: 157 loop : -0.31 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP L 36 PHE 0.017 0.002 PHE H 110 TYR 0.023 0.001 TYR L 92 ARG 0.008 0.001 ARG L 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 76 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.7003 (pm20) cc_final: 0.6759 (pm20) REVERT: H 47 TRP cc_start: 0.8317 (t60) cc_final: 0.7863 (t60) REVERT: H 112 MET cc_start: 0.7897 (mpp) cc_final: 0.7341 (mpp) REVERT: L 17 GLU cc_start: 0.7647 (pm20) cc_final: 0.6863 (pm20) REVERT: L 37 TYR cc_start: 0.8402 (m-80) cc_final: 0.8198 (m-10) REVERT: L 93 ARG cc_start: 0.7823 (tpp-160) cc_final: 0.7319 (tpm170) REVERT: L 101 GLN cc_start: 0.8234 (mp10) cc_final: 0.7982 (mp10) outliers start: 24 outliers final: 23 residues processed: 88 average time/residue: 0.1768 time to fit residues: 18.4121 Evaluate side-chains 93 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 70 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 6 optimal weight: 0.1980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3336 Z= 0.211 Angle : 0.689 7.689 4544 Z= 0.343 Chirality : 0.047 0.188 501 Planarity : 0.006 0.089 588 Dihedral : 5.801 30.059 555 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 6.67 % Allowed : 25.71 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 (0.41), residues: 418 helix: -2.55 (0.84), residues: 33 sheet: -0.84 (0.40), residues: 156 loop : -0.29 (0.43), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP L 36 PHE 0.014 0.002 PHE H 27 TYR 0.019 0.001 TYR L 92 ARG 0.007 0.001 ARG L 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 74 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.6981 (pm20) cc_final: 0.6731 (pm20) REVERT: H 47 TRP cc_start: 0.8177 (t60) cc_final: 0.7851 (t60) REVERT: H 112 MET cc_start: 0.7856 (mpp) cc_final: 0.7363 (mpp) REVERT: L 17 GLU cc_start: 0.7614 (pm20) cc_final: 0.6873 (pm20) REVERT: L 37 TYR cc_start: 0.8326 (m-80) cc_final: 0.8124 (m-10) REVERT: L 93 ARG cc_start: 0.7864 (tpp-160) cc_final: 0.7294 (tpm170) REVERT: L 101 GLN cc_start: 0.8125 (mp10) cc_final: 0.7897 (mp10) REVERT: L 104 LYS cc_start: 0.8973 (ptmm) cc_final: 0.8758 (ptmm) outliers start: 21 outliers final: 20 residues processed: 85 average time/residue: 0.1712 time to fit residues: 17.4083 Evaluate side-chains 91 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 71 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.112520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.094804 restraints weight = 8643.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.097266 restraints weight = 5886.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.099014 restraints weight = 4478.208| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.207 3336 Z= 0.384 Angle : 1.409 59.200 4544 Z= 0.811 Chirality : 0.064 0.977 501 Planarity : 0.006 0.079 588 Dihedral : 5.827 29.774 555 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 6.98 % Allowed : 25.40 % Favored : 67.62 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.41), residues: 418 helix: -2.56 (0.84), residues: 33 sheet: -1.00 (0.39), residues: 160 loop : -0.17 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP L 36 PHE 0.014 0.002 PHE H 27 TYR 0.018 0.001 TYR L 92 ARG 0.005 0.001 ARG L 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1230.28 seconds wall clock time: 22 minutes 42.80 seconds (1362.80 seconds total)