Starting phenix.real_space_refine on Fri Dec 27 08:20:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ru4_24696/12_2024/7ru4_24696.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ru4_24696/12_2024/7ru4_24696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ru4_24696/12_2024/7ru4_24696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ru4_24696/12_2024/7ru4_24696.map" model { file = "/net/cci-nas-00/data/ceres_data/7ru4_24696/12_2024/7ru4_24696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ru4_24696/12_2024/7ru4_24696.cif" } resolution = 3.3 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= 0.016 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 14 5.16 5 C 2151 2.51 5 N 564 2.21 5 O 653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3382 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 894 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 826 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1610 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 1 Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.59, per 1000 atoms: 1.36 Number of scatterers: 3382 At special positions: 0 Unit cell: (64.89, 99.91, 84.46, 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 14 16.00 O 653 8.00 N 564 7.00 C 2151 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " BETA1-6 " NAG B 1 " - " FUC B 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG B 1 " - " ASN A 343 " Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 419.4 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 9 sheets defined 15.0% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.799A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.899A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.233A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.886A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.208A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 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 9 through 11 removed outlier: 4.048A pdb=" N ALA H 9 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR H 110 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 9 through 11 removed outlier: 4.048A pdb=" N ALA H 9 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR H 110 " --> pdb=" O ALA H 9 " (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: 6.482A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.500A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 127 hydrogen bonds defined for protein. 297 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: 0.93 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 949 1.33 - 1.47: 1110 1.47 - 1.61: 1385 1.61 - 1.74: 4 1.74 - 1.88: 16 Bond restraints: 3464 Sorted by residual: bond pdb=" CB ILE A 326 " pdb=" CG1 ILE A 326 " ideal model delta sigma weight residual 1.530 1.679 -0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" CG GLN L 6 " pdb=" CD GLN L 6 " ideal model delta sigma weight residual 1.516 1.384 0.132 2.50e-02 1.60e+03 2.79e+01 bond pdb=" CB TYR L 87 " pdb=" CG TYR L 87 " ideal model delta sigma weight residual 1.512 1.397 0.115 2.20e-02 2.07e+03 2.75e+01 bond pdb=" CB TYR L 36 " pdb=" CG TYR L 36 " ideal model delta sigma weight residual 1.512 1.398 0.114 2.20e-02 2.07e+03 2.67e+01 bond pdb=" CB ILE A 472 " pdb=" CG2 ILE A 472 " ideal model delta sigma weight residual 1.521 1.363 0.158 3.30e-02 9.18e+02 2.29e+01 ... (remaining 3459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 4038 2.58 - 5.15: 576 5.15 - 7.73: 72 7.73 - 10.30: 16 10.30 - 12.88: 4 Bond angle restraints: 4706 Sorted by residual: angle pdb=" N ARG L 61 " pdb=" CA ARG L 61 " pdb=" C ARG L 61 " ideal model delta sigma weight residual 114.56 101.68 12.88 1.27e+00 6.20e-01 1.03e+02 angle pdb=" N ALA A 520 " pdb=" CA ALA A 520 " pdb=" C ALA A 520 " ideal model delta sigma weight residual 108.13 117.09 -8.96 9.00e-01 1.23e+00 9.91e+01 angle pdb=" N LEU H 54 " pdb=" CA LEU H 54 " pdb=" C LEU H 54 " ideal model delta sigma weight residual 113.97 102.00 11.97 1.28e+00 6.10e-01 8.75e+01 angle pdb=" N GLN A 474 " pdb=" CA GLN A 474 " pdb=" C GLN A 474 " ideal model delta sigma weight residual 110.55 122.38 -11.83 1.35e+00 5.49e-01 7.68e+01 angle pdb=" N PHE L 98 " pdb=" CA PHE L 98 " pdb=" C PHE L 98 " ideal model delta sigma weight residual 113.30 124.82 -11.52 1.34e+00 5.57e-01 7.39e+01 ... (remaining 4701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.72: 1998 14.72 - 29.45: 69 29.45 - 44.17: 15 44.17 - 58.90: 13 58.90 - 73.62: 4 Dihedral angle restraints: 2099 sinusoidal: 864 harmonic: 1235 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 138.11 -45.11 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 64.13 28.87 1 1.00e+01 1.00e-02 1.19e+01 dihedral pdb=" SG CYS A 391 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " pdb=" CA CYS A 525 " ideal model delta sinusoidal sigma weight residual 79.00 23.24 55.76 1 2.00e+01 2.50e-03 1.05e+01 ... (remaining 2096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 322 0.087 - 0.173: 141 0.173 - 0.260: 46 0.260 - 0.346: 11 0.346 - 0.433: 6 Chirality restraints: 526 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.08e+02 chirality pdb=" C1 FUC B 3 " pdb=" O6 NAG B 1 " pdb=" C2 FUC B 3 " pdb=" O5 FUC B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.98e+01 chirality pdb=" C2 NAG B 2 " pdb=" C1 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" N2 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.92 0.43 2.00e-01 2.50e+01 4.68e+00 ... (remaining 523 not shown) Planarity restraints: 599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " -0.057 2.00e-02 2.50e+03 2.67e-02 1.78e+01 pdb=" CG TRP H 47 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " 0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 32 " -0.056 2.00e-02 2.50e+03 2.94e-02 1.73e+01 pdb=" CG TYR L 32 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR L 32 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR L 32 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR L 32 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR L 32 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR L 32 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR L 32 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 478 " 0.018 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C THR A 478 " -0.060 2.00e-02 2.50e+03 pdb=" O THR A 478 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO A 479 " 0.020 2.00e-02 2.50e+03 ... (remaining 596 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1243 2.87 - 3.38: 2954 3.38 - 3.88: 5675 3.88 - 4.39: 6717 4.39 - 4.90: 10862 Nonbonded interactions: 27451 Sorted by model distance: nonbonded pdb=" OE1 GLU A 340 " pdb=" NZ LYS A 356 " model vdw 2.362 3.120 nonbonded pdb=" N LEU H 54 " pdb=" N ASP H 55 " model vdw 2.363 2.560 nonbonded pdb=" N ARG L 61 " pdb=" N PHE L 62 " model vdw 2.377 2.560 nonbonded pdb=" N PRO A 426 " pdb=" O PRO A 426 " model vdw 2.440 2.496 nonbonded pdb=" N GLN H 97 " pdb=" O GLN H 97 " model vdw 2.463 2.496 ... (remaining 27446 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.760 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.023 0.158 3464 Z= 1.507 Angle : 1.894 12.879 4706 Z= 1.262 Chirality : 0.113 0.433 526 Planarity : 0.008 0.035 597 Dihedral : 9.651 73.619 1295 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.55 % Allowed : 1.10 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.06 (0.40), residues: 420 helix: -3.40 (0.59), residues: 31 sheet: 1.34 (0.44), residues: 150 loop : -0.30 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.010 TRP H 47 HIS 0.003 0.002 HIS L 90 PHE 0.026 0.005 PHE A 374 TYR 0.056 0.008 TYR L 32 ARG 0.005 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 0.392 Fit side-chains REVERT: H 89 VAL cc_start: 0.9153 (t) cc_final: 0.8894 (p) REVERT: A 332 ILE cc_start: 0.8865 (mt) cc_final: 0.8380 (mt) REVERT: A 336 CYS cc_start: 0.6290 (m) cc_final: 0.5884 (m) REVERT: A 360 ASN cc_start: 0.8823 (t0) cc_final: 0.8398 (t0) REVERT: A 453 TYR cc_start: 0.5598 (m-80) cc_final: 0.5330 (m-80) REVERT: A 458 LYS cc_start: 0.7751 (pttt) cc_final: 0.7151 (mmtm) outliers start: 2 outliers final: 0 residues processed: 122 average time/residue: 0.2425 time to fit residues: 33.8088 Evaluate side-chains 75 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.2980 chunk 31 optimal weight: 0.0970 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 97 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3464 Z= 0.242 Angle : 0.747 10.120 4706 Z= 0.392 Chirality : 0.050 0.184 526 Planarity : 0.005 0.041 597 Dihedral : 5.821 25.559 549 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.11 % Allowed : 7.67 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.20 (0.40), residues: 420 helix: -1.67 (1.25), residues: 25 sheet: 0.83 (0.42), residues: 149 loop : -0.56 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.001 0.001 HIS L 90 PHE 0.009 0.001 PHE H 29 TYR 0.023 0.002 TYR A 495 ARG 0.006 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.341 Fit side-chains REVERT: H 100 LEU cc_start: 0.9294 (mt) cc_final: 0.9018 (mt) REVERT: L 21 LEU cc_start: 0.8907 (mm) cc_final: 0.8639 (mp) REVERT: A 328 ARG cc_start: 0.7377 (tpt90) cc_final: 0.4632 (pmt-80) REVERT: A 356 LYS cc_start: 0.8549 (tttt) cc_final: 0.7440 (tttt) REVERT: A 420 ASP cc_start: 0.6323 (m-30) cc_final: 0.5618 (t0) REVERT: A 458 LYS cc_start: 0.7723 (pttt) cc_final: 0.7026 (mmpt) REVERT: A 460 ASN cc_start: 0.6739 (m-40) cc_final: 0.6046 (m-40) outliers start: 15 outliers final: 7 residues processed: 100 average time/residue: 0.1667 time to fit residues: 20.1514 Evaluate side-chains 79 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 398 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 97 GLN H 105 GLN L 6 GLN L 100 GLN A 501 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 3464 Z= 0.300 Angle : 0.691 7.541 4706 Z= 0.363 Chirality : 0.049 0.214 526 Planarity : 0.005 0.044 597 Dihedral : 5.604 28.360 549 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.38 % Allowed : 12.05 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.40 (0.40), residues: 420 helix: -1.77 (1.18), residues: 25 sheet: 0.84 (0.42), residues: 150 loop : -0.83 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.019 0.002 PHE A 497 TYR 0.017 0.002 TYR A 453 ARG 0.005 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.396 Fit side-chains REVERT: H 4 LEU cc_start: 0.8103 (mt) cc_final: 0.7862 (mm) REVERT: L 21 LEU cc_start: 0.8936 (mm) cc_final: 0.8664 (mp) REVERT: L 49 TYR cc_start: 0.9087 (p90) cc_final: 0.8852 (p90) REVERT: A 328 ARG cc_start: 0.7435 (tpt90) cc_final: 0.4792 (pmt-80) REVERT: A 420 ASP cc_start: 0.6616 (m-30) cc_final: 0.5933 (t0) REVERT: A 458 LYS cc_start: 0.7618 (pttt) cc_final: 0.6996 (mmtt) REVERT: A 460 ASN cc_start: 0.6851 (m-40) cc_final: 0.6172 (m-40) outliers start: 16 outliers final: 9 residues processed: 87 average time/residue: 0.1528 time to fit residues: 16.2590 Evaluate side-chains 79 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 398 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 0.0570 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 0.0270 chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 97 GLN H 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3464 Z= 0.198 Angle : 0.656 9.027 4706 Z= 0.335 Chirality : 0.047 0.176 526 Planarity : 0.005 0.044 597 Dihedral : 5.386 27.236 549 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.38 % Allowed : 12.05 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.42 (0.40), residues: 420 helix: -2.16 (1.03), residues: 26 sheet: 0.85 (0.41), residues: 152 loop : -0.81 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 HIS 0.001 0.001 HIS L 90 PHE 0.009 0.001 PHE L 83 TYR 0.021 0.002 TYR A 495 ARG 0.004 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8166 (mt) cc_final: 0.7896 (mm) REVERT: H 110 THR cc_start: 0.8216 (p) cc_final: 0.7971 (p) REVERT: L 21 LEU cc_start: 0.8898 (mm) cc_final: 0.8622 (mp) REVERT: L 87 TYR cc_start: 0.6252 (p90) cc_final: 0.5967 (p90) REVERT: A 328 ARG cc_start: 0.7416 (tpt90) cc_final: 0.4860 (pmt-80) REVERT: A 392 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: A 420 ASP cc_start: 0.6488 (m-30) cc_final: 0.5800 (t0) REVERT: A 458 LYS cc_start: 0.7591 (pttt) cc_final: 0.6884 (mmpt) REVERT: A 460 ASN cc_start: 0.6813 (m-40) cc_final: 0.6167 (m-40) outliers start: 16 outliers final: 12 residues processed: 86 average time/residue: 0.1558 time to fit residues: 16.5206 Evaluate side-chains 82 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 97 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3464 Z= 0.292 Angle : 0.653 6.320 4706 Z= 0.341 Chirality : 0.048 0.203 526 Planarity : 0.005 0.042 597 Dihedral : 5.523 30.498 549 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.75 % Allowed : 12.33 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.62 (0.40), residues: 420 helix: -2.23 (1.00), residues: 26 sheet: 0.87 (0.41), residues: 152 loop : -1.09 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 103 HIS 0.001 0.001 HIS L 90 PHE 0.010 0.001 PHE A 486 TYR 0.018 0.002 TYR A 453 ARG 0.004 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8197 (mt) cc_final: 0.7927 (mm) REVERT: H 110 THR cc_start: 0.8172 (p) cc_final: 0.7903 (p) REVERT: L 21 LEU cc_start: 0.8851 (mm) cc_final: 0.8567 (mp) REVERT: A 340 GLU cc_start: 0.8444 (pt0) cc_final: 0.8189 (pt0) REVERT: A 356 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8466 (ttpt) REVERT: A 392 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7100 (m-80) REVERT: A 420 ASP cc_start: 0.6587 (m-30) cc_final: 0.5823 (t0) REVERT: A 453 TYR cc_start: 0.5253 (m-80) cc_final: 0.4786 (m-80) REVERT: A 458 LYS cc_start: 0.7553 (pttt) cc_final: 0.6834 (mmpt) REVERT: A 460 ASN cc_start: 0.6890 (m-40) cc_final: 0.6203 (m-40) outliers start: 21 outliers final: 13 residues processed: 85 average time/residue: 0.1591 time to fit residues: 16.4516 Evaluate side-chains 85 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 97 GLN H 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3464 Z= 0.222 Angle : 0.635 8.318 4706 Z= 0.328 Chirality : 0.047 0.205 526 Planarity : 0.005 0.043 597 Dihedral : 5.324 24.449 549 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 6.03 % Allowed : 12.88 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.63 (0.40), residues: 420 helix: -2.18 (1.01), residues: 26 sheet: 0.99 (0.41), residues: 152 loop : -1.20 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 103 HIS 0.001 0.001 HIS L 90 PHE 0.007 0.001 PHE L 83 TYR 0.015 0.002 TYR L 49 ARG 0.003 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8217 (mt) cc_final: 0.7954 (mm) REVERT: H 110 THR cc_start: 0.8179 (p) cc_final: 0.7901 (p) REVERT: L 21 LEU cc_start: 0.8845 (mm) cc_final: 0.8549 (mp) REVERT: L 24 ARG cc_start: 0.7038 (mmm-85) cc_final: 0.6810 (mmm-85) REVERT: A 340 GLU cc_start: 0.8457 (pt0) cc_final: 0.8191 (pt0) REVERT: A 356 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8401 (ttpt) REVERT: A 360 ASN cc_start: 0.8865 (t0) cc_final: 0.8656 (t0) REVERT: A 389 ASP cc_start: 0.7677 (m-30) cc_final: 0.7432 (m-30) REVERT: A 392 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.6898 (m-80) REVERT: A 420 ASP cc_start: 0.6606 (m-30) cc_final: 0.5814 (t0) REVERT: A 458 LYS cc_start: 0.7478 (pttt) cc_final: 0.6685 (mmpt) REVERT: A 460 ASN cc_start: 0.6931 (m-40) cc_final: 0.6237 (m-40) outliers start: 22 outliers final: 12 residues processed: 88 average time/residue: 0.1620 time to fit residues: 17.2501 Evaluate side-chains 91 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3464 Z= 0.253 Angle : 0.645 6.389 4706 Z= 0.334 Chirality : 0.047 0.189 526 Planarity : 0.005 0.041 597 Dihedral : 5.373 24.932 549 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.84 % Allowed : 15.07 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.40), residues: 420 helix: -2.17 (1.01), residues: 26 sheet: 1.05 (0.41), residues: 152 loop : -1.30 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 103 HIS 0.001 0.001 HIS L 90 PHE 0.009 0.001 PHE A 497 TYR 0.029 0.002 TYR A 453 ARG 0.003 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: H 110 THR cc_start: 0.8176 (p) cc_final: 0.7881 (p) REVERT: A 356 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8507 (ttpt) REVERT: A 389 ASP cc_start: 0.7619 (m-30) cc_final: 0.7394 (m-30) REVERT: A 392 PHE cc_start: 0.7567 (OUTLIER) cc_final: 0.6672 (m-80) REVERT: A 420 ASP cc_start: 0.6675 (m-30) cc_final: 0.5849 (t0) REVERT: A 458 LYS cc_start: 0.7502 (pttt) cc_final: 0.6690 (mmpt) REVERT: A 460 ASN cc_start: 0.7028 (m-40) cc_final: 0.6315 (m-40) outliers start: 14 outliers final: 11 residues processed: 78 average time/residue: 0.1740 time to fit residues: 16.4823 Evaluate side-chains 88 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.0670 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.0050 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.3932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 97 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3464 Z= 0.189 Angle : 0.628 6.719 4706 Z= 0.321 Chirality : 0.046 0.133 526 Planarity : 0.005 0.041 597 Dihedral : 5.092 24.690 549 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.29 % Allowed : 16.16 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.41), residues: 420 helix: -2.16 (1.02), residues: 26 sheet: 1.20 (0.42), residues: 152 loop : -1.30 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 98 HIS 0.001 0.000 HIS A 519 PHE 0.007 0.001 PHE A 497 TYR 0.025 0.002 TYR L 49 ARG 0.003 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: H 110 THR cc_start: 0.8090 (p) cc_final: 0.7806 (p) REVERT: L 21 LEU cc_start: 0.8833 (mm) cc_final: 0.8533 (mp) REVERT: A 340 GLU cc_start: 0.8266 (pt0) cc_final: 0.7685 (pp20) REVERT: A 356 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.7245 (ttpt) REVERT: A 392 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.6589 (m-80) REVERT: A 420 ASP cc_start: 0.6702 (m-30) cc_final: 0.5870 (t0) REVERT: A 458 LYS cc_start: 0.7477 (pttt) cc_final: 0.6654 (mmpt) REVERT: A 460 ASN cc_start: 0.6985 (m-40) cc_final: 0.6286 (m-40) outliers start: 12 outliers final: 9 residues processed: 85 average time/residue: 0.1757 time to fit residues: 17.9390 Evaluate side-chains 85 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.0030 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.0000 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3464 Z= 0.213 Angle : 0.673 11.370 4706 Z= 0.345 Chirality : 0.048 0.187 526 Planarity : 0.005 0.040 597 Dihedral : 5.454 28.801 549 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.56 % Allowed : 17.53 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.61 (0.41), residues: 420 helix: -2.26 (0.99), residues: 26 sheet: 1.20 (0.43), residues: 152 loop : -1.34 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 98 HIS 0.001 0.001 HIS L 90 PHE 0.006 0.001 PHE A 486 TYR 0.025 0.002 TYR L 49 ARG 0.003 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: H 110 THR cc_start: 0.8107 (p) cc_final: 0.7823 (p) REVERT: L 21 LEU cc_start: 0.8837 (mm) cc_final: 0.8532 (mp) REVERT: A 340 GLU cc_start: 0.8350 (pt0) cc_final: 0.7792 (pp20) REVERT: A 356 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.7103 (ttpt) REVERT: A 392 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.6092 (m-80) REVERT: A 420 ASP cc_start: 0.6735 (m-30) cc_final: 0.5908 (t0) REVERT: A 458 LYS cc_start: 0.7359 (pttt) cc_final: 0.6584 (mmpt) REVERT: A 460 ASN cc_start: 0.7028 (m-40) cc_final: 0.6316 (m-40) outliers start: 13 outliers final: 8 residues processed: 78 average time/residue: 0.1661 time to fit residues: 15.8309 Evaluate side-chains 86 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 97 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3464 Z= 0.250 Angle : 0.695 10.377 4706 Z= 0.360 Chirality : 0.048 0.183 526 Planarity : 0.005 0.038 597 Dihedral : 5.561 28.384 549 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.01 % Allowed : 18.08 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.77 (0.41), residues: 420 helix: -2.43 (0.96), residues: 26 sheet: 1.18 (0.43), residues: 150 loop : -1.49 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 98 HIS 0.001 0.001 HIS L 90 PHE 0.008 0.001 PHE A 497 TYR 0.025 0.002 TYR A 453 ARG 0.003 0.001 ARG L 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: H 110 THR cc_start: 0.8154 (p) cc_final: 0.7948 (p) REVERT: L 21 LEU cc_start: 0.8829 (mm) cc_final: 0.8501 (mp) REVERT: A 340 GLU cc_start: 0.8399 (pt0) cc_final: 0.7873 (pp20) REVERT: A 356 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.7204 (ttpt) REVERT: A 386 LYS cc_start: 0.4525 (mttt) cc_final: 0.3628 (mtpt) REVERT: A 458 LYS cc_start: 0.7280 (pttt) cc_final: 0.6501 (mmpt) outliers start: 11 outliers final: 8 residues processed: 77 average time/residue: 0.1531 time to fit residues: 14.4992 Evaluate side-chains 83 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 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 = 0.3513 r_free = 0.3513 target = 0.087539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.080234 restraints weight = 9638.855| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.76 r_work: 0.3278 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3464 Z= 0.219 Angle : 0.673 9.912 4706 Z= 0.348 Chirality : 0.047 0.178 526 Planarity : 0.005 0.037 597 Dihedral : 5.401 28.785 549 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.47 % Allowed : 19.18 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.86 (0.41), residues: 420 helix: -2.57 (0.94), residues: 26 sheet: 1.08 (0.43), residues: 150 loop : -1.51 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 98 HIS 0.001 0.000 HIS L 90 PHE 0.032 0.001 PHE H 79 TYR 0.022 0.002 TYR A 495 ARG 0.003 0.001 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1451.75 seconds wall clock time: 26 minutes 51.80 seconds (1611.80 seconds total)