Starting phenix.real_space_refine on Wed Mar 12 01:13:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dtk_27703/03_2025/8dtk_27703_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dtk_27703/03_2025/8dtk_27703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dtk_27703/03_2025/8dtk_27703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dtk_27703/03_2025/8dtk_27703.map" model { file = "/net/cci-nas-00/data/ceres_data/8dtk_27703/03_2025/8dtk_27703_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dtk_27703/03_2025/8dtk_27703_neut_trim.cif" } resolution = 3.77 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= -0.004 sd= 0.034 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: 5 Type Number sf(0) Gaussians S 15 5.16 5 C 2248 2.51 5 N 596 2.21 5 O 692 1.98 5 H 3363 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6914 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3134 Classifications: {'peptide': 203} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 11, 'TRANS': 191} Chain: "B" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1749 Classifications: {'peptide': 113} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 106} Chain: "C" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2003 Classifications: {'peptide': 133} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 129} 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: 4.20, per 1000 atoms: 0.61 Number of scatterers: 6914 At special positions: 0 Unit cell: (69.828, 92.046, 85.698, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 O 692 8.00 N 596 7.00 C 2248 6.00 H 3363 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 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=2.03 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 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " 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 NAG-ASN " NAG A 601 " - " ASN A 331 " " NAG A 602 " - " ASN A 343 " Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 595.4 milliseconds 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 11.4% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.753A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.151A 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 502 through 505 Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.571A pdb=" N GLN C 64 " --> pdb=" O GLN C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.666A pdb=" N THR C 87 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.909A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.909A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.853A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 5 removed outlier: 3.839A pdb=" N THR B 5 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG B 24 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 67 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.551A pdb=" N VAL B 85 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.968A pdb=" N VAL C 5 " --> pdb=" O GLN C 23 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN C 23 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 78 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.637A pdb=" N GLU C 10 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C 110 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 17 through 18 removed outlier: 3.543A pdb=" N VAL C 18 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU C 82 " --> pdb=" O VAL C 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 78 hydrogen bonds defined for protein. 177 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: 2.60 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3363 1.03 - 1.23: 9 1.23 - 1.42: 1608 1.42 - 1.62: 2005 1.62 - 1.81: 18 Bond restraints: 7003 Sorted by residual: bond pdb=" CB GLU C 81 " pdb=" CG GLU C 81 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.12e+00 bond pdb=" CB ASP C 95 " pdb=" CG ASP C 95 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.66e+00 bond pdb=" CB ASP B 9 " pdb=" CG ASP B 9 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.56e+00 bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.46e+00 bond pdb=" CB MET B 4 " pdb=" CG MET B 4 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.34e+00 ... (remaining 6998 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.57: 12528 7.57 - 15.13: 2 15.13 - 22.70: 1 22.70 - 30.26: 2 30.26 - 37.83: 3 Bond angle restraints: 12536 Sorted by residual: angle pdb=" C PHE C 100N" pdb=" CA PHE C 100N" pdb=" HA PHE C 100N" ideal model delta sigma weight residual 109.00 71.17 37.83 3.00e+00 1.11e-01 1.59e+02 angle pdb=" N PHE C 100N" pdb=" CA PHE C 100N" pdb=" HA PHE C 100N" ideal model delta sigma weight residual 110.00 74.48 35.52 3.00e+00 1.11e-01 1.40e+02 angle pdb=" CB PHE C 100N" pdb=" CA PHE C 100N" pdb=" HA PHE C 100N" ideal model delta sigma weight residual 109.00 78.57 30.43 3.00e+00 1.11e-01 1.03e+02 angle pdb=" CB LEU C 4 " pdb=" CG LEU C 4 " pdb=" HG LEU C 4 " ideal model delta sigma weight residual 109.00 85.17 23.83 3.00e+00 1.11e-01 6.31e+01 angle pdb=" CD2 LEU C 4 " pdb=" CG LEU C 4 " pdb=" HG LEU C 4 " ideal model delta sigma weight residual 108.00 84.21 23.79 3.00e+00 1.11e-01 6.29e+01 ... (remaining 12531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.08: 3126 22.08 - 44.16: 208 44.16 - 66.23: 51 66.23 - 88.31: 15 88.31 - 110.39: 5 Dihedral angle restraints: 3405 sinusoidal: 1818 harmonic: 1587 Sorted by residual: dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual -180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA VAL A 524 " pdb=" C VAL A 524 " pdb=" N CYS A 525 " pdb=" CA CYS A 525 " ideal model delta harmonic sigma weight residual 180.00 -155.80 -24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 125.03 -32.03 1 1.00e+01 1.00e-02 1.46e+01 ... (remaining 3402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.352: 537 0.352 - 0.705: 0 0.705 - 1.057: 0 1.057 - 1.409: 0 1.409 - 1.762: 1 Chirality restraints: 538 Sorted by residual: chirality pdb=" CG LEU C 4 " pdb=" CB LEU C 4 " pdb=" CD1 LEU C 4 " pdb=" CD2 LEU C 4 " both_signs ideal model delta sigma weight residual False -2.59 -0.83 -1.76 2.00e-01 2.50e+01 7.76e+01 chirality pdb=" CA PHE C 100N" pdb=" N PHE C 100N" pdb=" C PHE C 100N" pdb=" CB PHE C 100N" both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA ILE B 48 " pdb=" N ILE B 48 " pdb=" C ILE B 48 " pdb=" CB ILE B 48 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.28e-01 ... (remaining 535 not shown) Planarity restraints: 1068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 61 " 0.214 9.50e-02 1.11e+02 7.17e-02 6.49e+00 pdb=" NE ARG B 61 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 61 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 61 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 61 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 61 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG B 61 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG B 61 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 61 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 497 " 0.013 2.00e-02 2.50e+03 1.04e-02 3.23e+00 pdb=" CG PHE A 497 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 497 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 497 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 497 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 497 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 497 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 497 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE A 497 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE A 497 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 497 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 497 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 13 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO C 14 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " 0.024 5.00e-02 4.00e+02 ... (remaining 1065 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 838 2.24 - 2.83: 14848 2.83 - 3.42: 17054 3.42 - 4.01: 23693 4.01 - 4.60: 35931 Nonbonded interactions: 92364 Sorted by model distance: nonbonded pdb=" H PHE C 100N" pdb=" HA PHE C 100N" model vdw 1.653 1.816 nonbonded pdb=" HA PHE C 100N" pdb=" HB2 PHE C 100N" model vdw 1.710 1.952 nonbonded pdb=" H ALA A 363 " pdb=" O CYS A 525 " model vdw 1.732 2.450 nonbonded pdb="HH12 ARG A 454 " pdb=" O SER A 469 " model vdw 1.739 2.450 nonbonded pdb=" O VAL C 96 " pdb=" HG1 THR C 100L" model vdw 1.744 2.450 ... (remaining 92359 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 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: 2.500 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: 0.120 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.280 Find NCS groups from input model: 0.040 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 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 : 0.005 0.044 3640 Z= 0.305 Angle : 0.788 10.998 4953 Z= 0.414 Chirality : 0.091 1.762 538 Planarity : 0.006 0.095 640 Dihedral : 16.060 110.391 1326 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.37), residues: 443 helix: -3.24 (0.52), residues: 40 sheet: -1.95 (0.44), residues: 124 loop : -1.00 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 100B HIS 0.005 0.002 HIS C 32 PHE 0.031 0.002 PHE A 497 TYR 0.021 0.002 TYR B 49 ARG 0.016 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.3440 time to fit residues: 34.9810 Evaluate side-chains 69 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 388 ASN B 42 GLN ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.185640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.161219 restraints weight = 11812.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.167609 restraints weight = 6127.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.171652 restraints weight = 3858.582| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3640 Z= 0.285 Angle : 0.670 10.354 4953 Z= 0.345 Chirality : 0.089 1.741 538 Planarity : 0.005 0.042 640 Dihedral : 9.041 58.143 541 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.78 % Allowed : 8.31 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.37), residues: 443 helix: -3.17 (0.58), residues: 40 sheet: -1.83 (0.47), residues: 108 loop : -1.14 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 100B HIS 0.004 0.002 HIS C 32 PHE 0.016 0.001 PHE A 490 TYR 0.014 0.001 TYR B 49 ARG 0.006 0.001 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 77 average time/residue: 0.3266 time to fit residues: 30.7688 Evaluate side-chains 74 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 36 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.185031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.161023 restraints weight = 11974.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.167392 restraints weight = 6089.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.171521 restraints weight = 3810.363| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3640 Z= 0.199 Angle : 0.578 10.146 4953 Z= 0.297 Chirality : 0.088 1.735 538 Planarity : 0.004 0.041 640 Dihedral : 7.320 57.686 541 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.04 % Allowed : 9.35 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.37), residues: 443 helix: -3.18 (0.58), residues: 40 sheet: -1.92 (0.47), residues: 109 loop : -1.09 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 47 HIS 0.003 0.001 HIS C 32 PHE 0.009 0.001 PHE A 490 TYR 0.012 0.001 TYR B 49 ARG 0.005 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 77 average time/residue: 0.3481 time to fit residues: 32.4120 Evaluate side-chains 72 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 32 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 0.0980 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.182058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.159022 restraints weight = 12115.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.164961 restraints weight = 6471.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.168719 restraints weight = 4141.184| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3640 Z= 0.245 Angle : 0.586 10.378 4953 Z= 0.302 Chirality : 0.087 1.739 538 Planarity : 0.004 0.047 640 Dihedral : 6.979 53.251 541 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.04 % Allowed : 11.95 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.36), residues: 443 helix: -3.22 (0.56), residues: 40 sheet: -1.70 (0.51), residues: 91 loop : -1.27 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 35 HIS 0.004 0.002 HIS C 32 PHE 0.011 0.001 PHE A 429 TYR 0.013 0.001 TYR B 49 ARG 0.006 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 75 average time/residue: 0.3938 time to fit residues: 35.1388 Evaluate side-chains 73 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 30 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.179173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.157129 restraints weight = 12035.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.162491 restraints weight = 6632.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.165981 restraints weight = 4365.524| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3640 Z= 0.258 Angle : 0.593 10.525 4953 Z= 0.304 Chirality : 0.088 1.754 538 Planarity : 0.004 0.049 640 Dihedral : 6.669 53.692 541 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.04 % Allowed : 13.25 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.37), residues: 443 helix: -2.80 (0.72), residues: 33 sheet: -1.64 (0.52), residues: 91 loop : -1.38 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 103 HIS 0.004 0.002 HIS C 32 PHE 0.011 0.001 PHE A 429 TYR 0.016 0.001 TYR B 49 ARG 0.007 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 75 average time/residue: 0.3622 time to fit residues: 32.7735 Evaluate side-chains 73 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 2 optimal weight: 0.0570 chunk 33 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.177392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.153071 restraints weight = 12484.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.159206 restraints weight = 6454.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.163103 restraints weight = 4074.241| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3640 Z= 0.211 Angle : 0.567 10.492 4953 Z= 0.289 Chirality : 0.088 1.751 538 Planarity : 0.004 0.055 640 Dihedral : 6.371 51.924 541 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.78 % Allowed : 14.29 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.37), residues: 443 helix: -2.68 (0.73), residues: 33 sheet: -1.43 (0.49), residues: 102 loop : -1.47 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 100B HIS 0.003 0.001 HIS C 32 PHE 0.006 0.001 PHE C 29 TYR 0.013 0.001 TYR B 49 ARG 0.008 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 75 average time/residue: 0.3549 time to fit residues: 32.1405 Evaluate side-chains 73 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 10 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: B 27 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.173007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.149689 restraints weight = 12442.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.155290 restraints weight = 6731.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.159038 restraints weight = 4378.824| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3640 Z= 0.327 Angle : 0.630 10.769 4953 Z= 0.325 Chirality : 0.089 1.766 538 Planarity : 0.005 0.062 640 Dihedral : 6.922 56.261 541 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.74 % Favored : 88.26 % Rotamer: Outliers : 1.04 % Allowed : 14.55 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.37), residues: 443 helix: -2.54 (0.82), residues: 27 sheet: -1.60 (0.48), residues: 105 loop : -1.60 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 103 HIS 0.005 0.002 HIS C 32 PHE 0.014 0.002 PHE C 29 TYR 0.014 0.002 TYR B 49 ARG 0.009 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 LYS cc_start: 0.7190 (tmtt) cc_final: 0.6914 (tmtt) REVERT: B 5 THR cc_start: 0.7597 (t) cc_final: 0.7381 (p) REVERT: C 38 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7776 (ttm170) outliers start: 4 outliers final: 3 residues processed: 76 average time/residue: 0.3647 time to fit residues: 33.3569 Evaluate side-chains 74 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 8 optimal weight: 0.0770 chunk 2 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.174705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.151736 restraints weight = 12533.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.157470 restraints weight = 6640.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.161101 restraints weight = 4244.383| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3640 Z= 0.230 Angle : 0.589 10.500 4953 Z= 0.300 Chirality : 0.088 1.757 538 Planarity : 0.004 0.068 640 Dihedral : 6.501 51.312 541 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 1.04 % Allowed : 15.84 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.37), residues: 443 helix: -2.65 (0.80), residues: 27 sheet: -1.50 (0.48), residues: 105 loop : -1.57 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 100B HIS 0.003 0.001 HIS C 32 PHE 0.011 0.001 PHE C 29 TYR 0.015 0.001 TYR B 49 ARG 0.010 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 529 LYS cc_start: 0.7241 (tmtt) cc_final: 0.6977 (tmtt) REVERT: B 5 THR cc_start: 0.7575 (t) cc_final: 0.7365 (p) REVERT: C 38 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7840 (ttm170) outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 0.3771 time to fit residues: 32.9887 Evaluate side-chains 73 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 8 optimal weight: 0.0670 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 0.0020 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 overall best weight: 0.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.177951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.155376 restraints weight = 12372.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.161200 restraints weight = 6490.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.164987 restraints weight = 4113.875| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3640 Z= 0.149 Angle : 0.548 10.365 4953 Z= 0.275 Chirality : 0.087 1.730 538 Planarity : 0.004 0.070 640 Dihedral : 5.934 47.684 541 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.78 % Allowed : 16.10 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.37), residues: 443 helix: -2.55 (0.81), residues: 27 sheet: -1.23 (0.49), residues: 103 loop : -1.46 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 100B HIS 0.004 0.002 HIS C 35 PHE 0.007 0.001 PHE A 497 TYR 0.012 0.001 TYR B 49 ARG 0.011 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 LYS cc_start: 0.7143 (tmtt) cc_final: 0.6913 (tmtt) REVERT: C 34 ILE cc_start: 0.9015 (tt) cc_final: 0.8631 (pt) outliers start: 3 outliers final: 3 residues processed: 74 average time/residue: 0.3556 time to fit residues: 32.1753 Evaluate side-chains 72 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.171898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148949 restraints weight = 12836.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.154649 restraints weight = 6856.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.158324 restraints weight = 4395.674| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3640 Z= 0.318 Angle : 0.625 10.450 4953 Z= 0.320 Chirality : 0.089 1.761 538 Planarity : 0.005 0.073 640 Dihedral : 6.590 55.846 541 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.19 % Favored : 87.81 % Rotamer: Outliers : 0.78 % Allowed : 15.58 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.37), residues: 443 helix: -2.49 (0.81), residues: 27 sheet: -1.39 (0.49), residues: 105 loop : -1.66 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 100B HIS 0.004 0.002 HIS C 32 PHE 0.018 0.002 PHE C 29 TYR 0.014 0.002 TYR B 49 ARG 0.011 0.001 ARG B 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 LYS cc_start: 0.7242 (tmtt) cc_final: 0.6972 (tmtt) outliers start: 3 outliers final: 3 residues processed: 74 average time/residue: 0.3490 time to fit residues: 31.2528 Evaluate side-chains 73 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 0.1980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.176387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.154056 restraints weight = 12514.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.159721 restraints weight = 6555.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.163501 restraints weight = 4187.283| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3640 Z= 0.162 Angle : 0.557 10.214 4953 Z= 0.280 Chirality : 0.087 1.734 538 Planarity : 0.005 0.076 640 Dihedral : 5.862 47.741 541 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.04 % Allowed : 15.32 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.38), residues: 443 helix: -2.46 (0.81), residues: 27 sheet: -1.18 (0.50), residues: 103 loop : -1.52 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 100B HIS 0.005 0.002 HIS C 35 PHE 0.007 0.001 PHE A 497 TYR 0.016 0.001 TYR B 49 ARG 0.011 0.001 ARG B 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3418.56 seconds wall clock time: 58 minutes 56.23 seconds (3536.23 seconds total)