Starting phenix.real_space_refine on Mon Mar 11 10:15:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2v_27151/03_2024/8d2v_27151_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2v_27151/03_2024/8d2v_27151.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2v_27151/03_2024/8d2v_27151_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2v_27151/03_2024/8d2v_27151_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2v_27151/03_2024/8d2v_27151_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2v_27151/03_2024/8d2v_27151.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2v_27151/03_2024/8d2v_27151.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2v_27151/03_2024/8d2v_27151_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2v_27151/03_2024/8d2v_27151_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1603 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 30 5.16 5 Na 1 4.78 5 C 4186 2.51 5 N 995 2.21 5 O 1175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6388 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3326 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 460, 3304 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 299 Unresolved non-hydrogen angles: 362 Unresolved non-hydrogen dihedrals: 245 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 157 Conformer: "B" Number of residues, atoms: 460, 3304 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 299 Unresolved non-hydrogen angles: 362 Unresolved non-hydrogen dihedrals: 245 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 157 bond proxies already assigned to first conformer: 3368 Chain: "B" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1375 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 14, 'TRANS': 186} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1371 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 12, 'TRANS': 190} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "A" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 316 Unusual residues: {' NA': 1, 'LMT': 8, 'ZGS': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 84 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 84 " occ=0.50 residue: pdb=" N APHE A 396 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 396 " occ=0.50 Time building chain proxies: 5.68, per 1000 atoms: 0.89 Number of scatterers: 6388 At special positions: 0 Unit cell: (71.74, 72.584, 141.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 1 15.00 Na 1 11.00 O 1175 8.00 N 995 7.00 C 4186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 86 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.7 seconds 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1568 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 8 sheets defined 41.3% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 37 through 67 Proline residue: A 49 - end of helix removed outlier: 3.783A pdb=" N GLY A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLN A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 99 Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 110 through 127 Proline residue: A 118 - end of helix removed outlier: 3.590A pdb=" N LEU A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 166 Proline residue: A 158 - end of helix removed outlier: 4.040A pdb=" N THR A 163 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N MET A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 199 Processing helix chain 'A' and resid 233 through 261 Processing helix chain 'A' and resid 278 through 287 Processing helix chain 'A' and resid 289 through 319 removed outlier: 3.579A pdb=" N LEU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU A 309 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY A 310 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 350 Proline residue: A 342 - end of helix Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.635A pdb=" N THR A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 378 through 413 Proline residue: A 399 - end of helix Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 420 through 450 removed outlier: 3.522A pdb=" N PHE A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 470 Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 494 through 506 removed outlier: 5.177A pdb=" N ASN A 499 " --> pdb=" O LYS A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 Processing sheet with id= A, first strand: chain 'B' and resid 10 through 12 removed outlier: 8.872A pdb=" N LYS B 11 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LYS B 100 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ASN B 36 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU B 45 " --> pdb=" O ASN B 36 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 18 through 23 Processing sheet with id= C, first strand: chain 'B' and resid 112 through 114 Processing sheet with id= D, first strand: chain 'B' and resid 140 through 144 Processing sheet with id= E, first strand: chain 'C' and resid 3 through 6 Processing sheet with id= F, first strand: chain 'C' and resid 109 through 111 removed outlier: 3.825A pdb=" N ALA C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 121 through 123 removed outlier: 3.628A pdb=" N VAL C 176 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N TRP C 170 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 184 through 187 removed outlier: 4.784A pdb=" N ALA C 184 " --> pdb=" O VAL C 200 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 1007 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: 2.11 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 964 1.31 - 1.44: 1856 1.44 - 1.56: 3666 1.56 - 1.69: 36 1.69 - 1.81: 42 Bond restraints: 6564 Sorted by residual: bond pdb=" C1B LMT A 609 " pdb=" O5B LMT A 609 " ideal model delta sigma weight residual 1.393 1.517 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C1B LMT A 606 " pdb=" O5B LMT A 606 " ideal model delta sigma weight residual 1.393 1.517 -0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C1B LMT A 605 " pdb=" O5B LMT A 605 " ideal model delta sigma weight residual 1.393 1.515 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C1B LMT A 604 " pdb=" O5B LMT A 604 " ideal model delta sigma weight residual 1.393 1.514 -0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" C1B LMT A 602 " pdb=" O5B LMT A 602 " ideal model delta sigma weight residual 1.393 1.512 -0.119 2.00e-02 2.50e+03 3.57e+01 ... (remaining 6559 not shown) Histogram of bond angle deviations from ideal: 86.72 - 99.86: 1 99.86 - 113.00: 3761 113.00 - 126.14: 5090 126.14 - 139.28: 134 139.28 - 152.42: 3 Bond angle restraints: 8989 Sorted by residual: angle pdb=" N GLY B 97 " pdb=" CA GLY B 97 " pdb=" C GLY B 97 " ideal model delta sigma weight residual 113.18 86.72 26.46 2.37e+00 1.78e-01 1.25e+02 angle pdb=" C04 ZGS A 601 " pdb=" C05 ZGS A 601 " pdb=" C06 ZGS A 601 " ideal model delta sigma weight residual 109.50 130.45 -20.95 3.00e+00 1.11e-01 4.88e+01 angle pdb=" C15 ZGS A 601 " pdb=" C16 ZGS A 601 " pdb=" C17 ZGS A 601 " ideal model delta sigma weight residual 109.50 122.06 -12.56 3.00e+00 1.11e-01 1.75e+01 angle pdb=" C29 ZGS A 601 " pdb=" C30 ZGS A 601 " pdb=" N31 ZGS A 601 " ideal model delta sigma weight residual 109.53 120.59 -11.06 3.00e+00 1.11e-01 1.36e+01 angle pdb=" N GLY C 191 " pdb=" CA GLY C 191 " pdb=" C GLY C 191 " ideal model delta sigma weight residual 112.73 108.63 4.10 1.20e+00 6.94e-01 1.17e+01 ... (remaining 8984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.59: 3669 26.59 - 53.18: 183 53.18 - 79.77: 65 79.77 - 106.36: 72 106.36 - 132.95: 55 Dihedral angle restraints: 4044 sinusoidal: 1584 harmonic: 2460 Sorted by residual: dihedral pdb=" C23 ZGS A 601 " pdb=" O24 ZGS A 601 " pdb=" P25 ZGS A 601 " pdb=" O26 ZGS A 601 " ideal model delta sinusoidal sigma weight residual -69.87 63.08 -132.95 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" C23 ZGS A 601 " pdb=" C21 ZGS A 601 " pdb=" C22 ZGS A 601 " pdb=" O20 ZGS A 601 " ideal model delta sinusoidal sigma weight residual -159.35 -34.94 -124.41 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" O2B LMT A 606 " pdb=" C2B LMT A 606 " pdb=" C3B LMT A 606 " pdb=" O3B LMT A 606 " ideal model delta sinusoidal sigma weight residual 63.73 -174.52 -121.75 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 4041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 858 0.058 - 0.116: 177 0.116 - 0.175: 28 0.175 - 0.233: 6 0.233 - 0.291: 1 Chirality restraints: 1070 Sorted by residual: chirality pdb=" C1B LMT A 607 " pdb=" C2B LMT A 607 " pdb=" O1B LMT A 607 " pdb=" O5B LMT A 607 " both_signs ideal model delta sigma weight residual False -2.20 -2.49 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C4' LMT A 606 " pdb=" C3' LMT A 606 " pdb=" C5' LMT A 606 " pdb=" O1B LMT A 606 " both_signs ideal model delta sigma weight residual False -2.55 -2.33 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C1B LMT A 602 " pdb=" C2B LMT A 602 " pdb=" O1B LMT A 602 " pdb=" O5B LMT A 602 " both_signs ideal model delta sigma weight residual False -2.20 -2.40 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1067 not shown) Planarity restraints: 1105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 103 " -0.048 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO C 104 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO C 104 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 104 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 46 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO C 47 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 47 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 47 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 75 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO B 76 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 76 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 76 " -0.031 5.00e-02 4.00e+02 ... (remaining 1102 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1527 2.79 - 3.32: 5636 3.32 - 3.84: 10739 3.84 - 4.37: 11389 4.37 - 4.90: 20293 Nonbonded interactions: 49584 Sorted by model distance: nonbonded pdb=" OE1 GLN A 62 " pdb=" OG1 THR A 444 " model vdw 2.262 2.440 nonbonded pdb=" N GLY B 97 " pdb=" O GLY B 97 " model vdw 2.279 2.496 nonbonded pdb=" OD2 ASP A 72 " pdb=" O6B LMT A 606 " model vdw 2.297 2.440 nonbonded pdb=" OH TYR A 129 " pdb=" O4' LMT A 605 " model vdw 2.308 2.440 nonbonded pdb=" O VAL A 332 " pdb=" OG SER A 336 " model vdw 2.310 2.440 ... (remaining 49579 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 5.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 11.370 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 24.980 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 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 : 0.010 0.124 6564 Z= 0.663 Angle : 1.137 26.456 8989 Z= 0.499 Chirality : 0.050 0.291 1070 Planarity : 0.007 0.073 1105 Dihedral : 28.590 132.951 2464 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.75 % Allowed : 7.12 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.27), residues: 862 helix: 0.05 (0.24), residues: 370 sheet: 0.01 (0.39), residues: 188 loop : -2.51 (0.31), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 140 HIS 0.001 0.000 HIS A 156 PHE 0.022 0.002 PHE B 89 TYR 0.018 0.002 TYR A 43 ARG 0.003 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 183 time to evaluate : 0.674 Fit side-chains REVERT: A 242 ILE cc_start: 0.8081 (mt) cc_final: 0.7616 (mm) REVERT: B 70 SER cc_start: 0.8046 (t) cc_final: 0.7226 (m) REVERT: B 72 SER cc_start: 0.8202 (m) cc_final: 0.7856 (p) REVERT: B 154 MET cc_start: 0.8205 (mtt) cc_final: 0.7539 (mtm) REVERT: B 156 TRP cc_start: 0.8406 (m-90) cc_final: 0.7857 (m-90) REVERT: C 81 ILE cc_start: 0.7687 (mm) cc_final: 0.7456 (mt) REVERT: C 136 THR cc_start: 0.9103 (m) cc_final: 0.8872 (p) REVERT: C 190 PHE cc_start: 0.7268 (t80) cc_final: 0.7053 (t80) outliers start: 3 outliers final: 0 residues processed: 185 average time/residue: 0.1589 time to fit residues: 39.6356 Evaluate side-chains 109 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 30.0000 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 78 optimal weight: 0.0170 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 234 GLN A 238 ASN A 328 ASN B 37 GLN B 153 ASN C 39 GLN C 99 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6564 Z= 0.302 Angle : 0.840 11.235 8989 Z= 0.380 Chirality : 0.056 0.649 1070 Planarity : 0.006 0.069 1105 Dihedral : 18.177 146.935 1416 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.19 % Allowed : 3.18 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.28), residues: 862 helix: 0.95 (0.26), residues: 371 sheet: -0.08 (0.41), residues: 177 loop : -2.38 (0.30), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 95 HIS 0.001 0.001 HIS A 156 PHE 0.036 0.002 PHE A 298 TYR 0.031 0.002 TYR A 358 ARG 0.004 0.000 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: A 264 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7400 (tm-30) REVERT: A 333 ILE cc_start: 0.8478 (mt) cc_final: 0.8252 (mm) REVERT: B 70 SER cc_start: 0.8049 (t) cc_final: 0.7212 (m) REVERT: B 72 SER cc_start: 0.8240 (m) cc_final: 0.7939 (p) REVERT: B 88 LEU cc_start: 0.7648 (pp) cc_final: 0.6149 (mp) REVERT: B 154 MET cc_start: 0.8164 (mtt) cc_final: 0.7746 (mtm) REVERT: B 156 TRP cc_start: 0.8535 (m-90) cc_final: 0.8121 (m-90) REVERT: C 72 GLN cc_start: 0.7994 (pm20) cc_final: 0.6490 (mt0) REVERT: C 81 ILE cc_start: 0.7667 (mm) cc_final: 0.7447 (mt) REVERT: C 112 ASN cc_start: 0.7587 (p0) cc_final: 0.7383 (p0) REVERT: C 136 THR cc_start: 0.9106 (m) cc_final: 0.8894 (p) REVERT: C 137 LEU cc_start: 0.8888 (mt) cc_final: 0.8659 (mt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1515 time to fit residues: 30.2578 Evaluate side-chains 114 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.0770 chunk 24 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 238 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6564 Z= 0.272 Angle : 0.719 7.179 8989 Z= 0.341 Chirality : 0.046 0.284 1070 Planarity : 0.006 0.073 1105 Dihedral : 12.572 134.882 1416 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.19 % Allowed : 2.25 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.29), residues: 862 helix: 1.11 (0.26), residues: 375 sheet: 0.03 (0.39), residues: 196 loop : -2.36 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 95 HIS 0.000 0.000 HIS A 156 PHE 0.029 0.002 PHE A 298 TYR 0.018 0.002 TYR A 291 ARG 0.003 0.001 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 SER cc_start: 0.8062 (t) cc_final: 0.7176 (m) REVERT: B 72 SER cc_start: 0.8223 (m) cc_final: 0.7964 (p) REVERT: B 88 LEU cc_start: 0.7589 (pp) cc_final: 0.6300 (mp) REVERT: C 72 GLN cc_start: 0.7922 (pm20) cc_final: 0.6773 (mt0) REVERT: C 81 ILE cc_start: 0.7610 (mm) cc_final: 0.7376 (mt) REVERT: C 137 LEU cc_start: 0.8913 (mt) cc_final: 0.8688 (mt) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1690 time to fit residues: 32.6298 Evaluate side-chains 106 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 8 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.0870 chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 41 optimal weight: 0.1980 chunk 74 optimal weight: 0.4980 chunk 22 optimal weight: 50.0000 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6564 Z= 0.176 Angle : 0.647 7.423 8989 Z= 0.308 Chirality : 0.044 0.273 1070 Planarity : 0.005 0.060 1105 Dihedral : 11.317 131.411 1416 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.19 % Allowed : 2.06 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.29), residues: 862 helix: 1.40 (0.27), residues: 373 sheet: -0.02 (0.41), residues: 178 loop : -2.23 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 344 HIS 0.001 0.000 HIS A 156 PHE 0.028 0.002 PHE A 486 TYR 0.034 0.002 TYR A 358 ARG 0.005 0.001 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TRP cc_start: 0.8430 (t-100) cc_final: 0.8194 (t-100) REVERT: A 382 TYR cc_start: 0.8519 (m-10) cc_final: 0.8281 (m-80) REVERT: A 462 GLU cc_start: 0.8323 (mp0) cc_final: 0.7653 (mt-10) REVERT: B 70 SER cc_start: 0.7971 (t) cc_final: 0.7102 (m) REVERT: B 72 SER cc_start: 0.8184 (m) cc_final: 0.7921 (p) REVERT: B 88 LEU cc_start: 0.7469 (pp) cc_final: 0.6455 (mp) REVERT: B 154 MET cc_start: 0.8279 (mtt) cc_final: 0.7790 (mtm) REVERT: C 72 GLN cc_start: 0.7944 (pm20) cc_final: 0.7023 (mt0) REVERT: C 81 ILE cc_start: 0.7677 (mm) cc_final: 0.7391 (mm) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1488 time to fit residues: 29.1839 Evaluate side-chains 107 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6564 Z= 0.257 Angle : 0.688 6.866 8989 Z= 0.330 Chirality : 0.045 0.273 1070 Planarity : 0.005 0.063 1105 Dihedral : 11.001 126.689 1416 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.19 % Allowed : 2.62 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.29), residues: 862 helix: 1.49 (0.27), residues: 373 sheet: -0.13 (0.40), residues: 175 loop : -2.23 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 95 HIS 0.000 0.000 HIS A 156 PHE 0.032 0.002 PHE A 427 TYR 0.016 0.002 TYR A 291 ARG 0.004 0.001 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 TRP cc_start: 0.8404 (t-100) cc_final: 0.8146 (t-100) REVERT: A 109 MET cc_start: 0.7825 (mmp) cc_final: 0.7612 (mmp) REVERT: A 385 SER cc_start: 0.7842 (t) cc_final: 0.7495 (p) REVERT: B 70 SER cc_start: 0.8039 (t) cc_final: 0.7147 (m) REVERT: B 72 SER cc_start: 0.8263 (m) cc_final: 0.7987 (p) REVERT: C 72 GLN cc_start: 0.8065 (pm20) cc_final: 0.6647 (mt0) REVERT: C 81 ILE cc_start: 0.7618 (mm) cc_final: 0.7388 (mm) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1375 time to fit residues: 25.4925 Evaluate side-chains 102 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 48 optimal weight: 0.0030 chunk 20 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6564 Z= 0.206 Angle : 0.656 6.709 8989 Z= 0.314 Chirality : 0.043 0.276 1070 Planarity : 0.005 0.058 1105 Dihedral : 10.394 108.765 1416 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.19 % Allowed : 1.31 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.29), residues: 862 helix: 1.56 (0.27), residues: 373 sheet: -0.17 (0.39), residues: 175 loop : -2.16 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 106 HIS 0.000 0.000 HIS A 230 PHE 0.029 0.002 PHE A 431 TYR 0.018 0.001 TYR A 291 ARG 0.004 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 TRP cc_start: 0.8404 (t-100) cc_final: 0.8174 (t-100) REVERT: A 359 ILE cc_start: 0.9121 (tp) cc_final: 0.8871 (mt) REVERT: A 385 SER cc_start: 0.7855 (t) cc_final: 0.7500 (p) REVERT: A 462 GLU cc_start: 0.8380 (mp0) cc_final: 0.7746 (mt-10) REVERT: B 70 SER cc_start: 0.7904 (t) cc_final: 0.7026 (m) REVERT: B 72 SER cc_start: 0.8183 (m) cc_final: 0.7968 (p) REVERT: C 72 GLN cc_start: 0.8098 (pm20) cc_final: 0.6972 (mt0) REVERT: C 81 ILE cc_start: 0.7675 (mm) cc_final: 0.7364 (mt) REVERT: C 190 PHE cc_start: 0.7876 (t80) cc_final: 0.7672 (t80) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1407 time to fit residues: 26.6223 Evaluate side-chains 103 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 0.1980 chunk 60 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6564 Z= 0.212 Angle : 0.651 6.555 8989 Z= 0.313 Chirality : 0.043 0.275 1070 Planarity : 0.005 0.057 1105 Dihedral : 9.951 110.612 1416 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.19 % Allowed : 0.75 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.29), residues: 862 helix: 1.61 (0.27), residues: 375 sheet: -0.21 (0.39), residues: 175 loop : -2.13 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 106 HIS 0.000 0.000 HIS A 156 PHE 0.037 0.002 PHE A 431 TYR 0.035 0.002 TYR A 358 ARG 0.004 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 TRP cc_start: 0.8387 (t-100) cc_final: 0.8152 (t-100) REVERT: A 334 MET cc_start: 0.7294 (mmm) cc_final: 0.6994 (mmp) REVERT: A 358 TYR cc_start: 0.8722 (m-80) cc_final: 0.8519 (m-80) REVERT: A 359 ILE cc_start: 0.9106 (tp) cc_final: 0.8858 (mt) REVERT: A 462 GLU cc_start: 0.8385 (mp0) cc_final: 0.7741 (mt-10) REVERT: A 483 LEU cc_start: 0.8584 (tp) cc_final: 0.8384 (tt) REVERT: B 70 SER cc_start: 0.7883 (t) cc_final: 0.6969 (m) REVERT: C 72 GLN cc_start: 0.8064 (pm20) cc_final: 0.6896 (mt0) REVERT: C 81 ILE cc_start: 0.7628 (mm) cc_final: 0.7386 (mt) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1447 time to fit residues: 26.1737 Evaluate side-chains 100 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 56 optimal weight: 0.1980 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 328 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6564 Z= 0.216 Angle : 0.656 6.979 8989 Z= 0.313 Chirality : 0.043 0.275 1070 Planarity : 0.005 0.054 1105 Dihedral : 9.684 108.861 1416 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.19 % Allowed : 1.31 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.29), residues: 862 helix: 1.65 (0.27), residues: 374 sheet: -0.15 (0.39), residues: 175 loop : -2.11 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 106 HIS 0.000 0.000 HIS A 156 PHE 0.036 0.002 PHE A 431 TYR 0.034 0.002 TYR A 358 ARG 0.005 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 TRP cc_start: 0.8398 (t-100) cc_final: 0.8162 (t-100) REVERT: A 181 MET cc_start: 0.8435 (mmm) cc_final: 0.8179 (tpp) REVERT: A 242 ILE cc_start: 0.8163 (mm) cc_final: 0.7952 (mm) REVERT: A 333 ILE cc_start: 0.8285 (mm) cc_final: 0.7939 (mm) REVERT: A 359 ILE cc_start: 0.9113 (tp) cc_final: 0.8868 (mt) REVERT: A 462 GLU cc_start: 0.8374 (mp0) cc_final: 0.7729 (mt-10) REVERT: B 7 PRO cc_start: 0.7662 (Cg_endo) cc_final: 0.7417 (Cg_exo) REVERT: B 70 SER cc_start: 0.7848 (t) cc_final: 0.7077 (m) REVERT: B 88 LEU cc_start: 0.7322 (pp) cc_final: 0.6622 (mp) REVERT: B 156 TRP cc_start: 0.8817 (m-90) cc_final: 0.8557 (m-90) REVERT: C 72 GLN cc_start: 0.8068 (pm20) cc_final: 0.6928 (mt0) REVERT: C 81 ILE cc_start: 0.7685 (mm) cc_final: 0.7373 (mt) REVERT: C 190 PHE cc_start: 0.7977 (t80) cc_final: 0.7653 (t80) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1444 time to fit residues: 25.3707 Evaluate side-chains 106 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 60 optimal weight: 0.0980 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 76 optimal weight: 0.2980 chunk 50 optimal weight: 0.0970 chunk 81 optimal weight: 0.0470 chunk 49 optimal weight: 0.5980 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 328 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6564 Z= 0.169 Angle : 0.625 7.004 8989 Z= 0.296 Chirality : 0.042 0.275 1070 Planarity : 0.005 0.054 1105 Dihedral : 9.196 105.135 1416 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.19 % Allowed : 0.75 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.29), residues: 862 helix: 1.68 (0.27), residues: 373 sheet: -0.05 (0.39), residues: 175 loop : -2.01 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 344 HIS 0.001 0.000 HIS A 156 PHE 0.032 0.002 PHE A 431 TYR 0.019 0.001 TYR A 291 ARG 0.006 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 CYS cc_start: 0.7986 (m) cc_final: 0.7581 (m) REVERT: A 103 TRP cc_start: 0.8412 (t-100) cc_final: 0.8167 (t-100) REVERT: A 181 MET cc_start: 0.8363 (mmm) cc_final: 0.8004 (tpp) REVERT: A 294 LEU cc_start: 0.8529 (tp) cc_final: 0.8233 (tt) REVERT: A 359 ILE cc_start: 0.9125 (tp) cc_final: 0.8876 (mt) REVERT: A 462 GLU cc_start: 0.8337 (mp0) cc_final: 0.7655 (mt-10) REVERT: B 7 PRO cc_start: 0.7545 (Cg_endo) cc_final: 0.7282 (Cg_exo) REVERT: B 70 SER cc_start: 0.7685 (t) cc_final: 0.6877 (m) REVERT: B 88 LEU cc_start: 0.7268 (pp) cc_final: 0.6729 (mp) REVERT: B 154 MET cc_start: 0.8139 (mtt) cc_final: 0.7903 (mtt) REVERT: B 156 TRP cc_start: 0.8728 (m-90) cc_final: 0.8457 (m-90) REVERT: C 72 GLN cc_start: 0.7945 (pm20) cc_final: 0.6897 (mt0) REVERT: C 81 ILE cc_start: 0.7646 (mm) cc_final: 0.7334 (mm) REVERT: C 190 PHE cc_start: 0.7972 (t80) cc_final: 0.7522 (t80) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1505 time to fit residues: 27.9788 Evaluate side-chains 106 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.8980 chunk 56 optimal weight: 0.1980 chunk 85 optimal weight: 1.9990 chunk 78 optimal weight: 0.0570 chunk 68 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 72 optimal weight: 0.0170 chunk 20 optimal weight: 0.3980 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6564 Z= 0.169 Angle : 0.619 6.967 8989 Z= 0.293 Chirality : 0.042 0.271 1070 Planarity : 0.005 0.054 1105 Dihedral : 8.899 100.877 1416 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.19 % Allowed : 0.56 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.29), residues: 862 helix: 1.76 (0.27), residues: 372 sheet: 0.05 (0.40), residues: 173 loop : -2.01 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 46 HIS 0.000 0.000 HIS A 156 PHE 0.031 0.001 PHE A 431 TYR 0.014 0.001 TYR C 123 ARG 0.006 0.000 ARG B 191 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 CYS cc_start: 0.7984 (m) cc_final: 0.7548 (m) REVERT: A 103 TRP cc_start: 0.8396 (t-100) cc_final: 0.8160 (t-100) REVERT: A 181 MET cc_start: 0.8323 (mmm) cc_final: 0.7912 (tpp) REVERT: A 359 ILE cc_start: 0.9132 (tp) cc_final: 0.8874 (mt) REVERT: A 462 GLU cc_start: 0.8340 (mp0) cc_final: 0.7734 (mt-10) REVERT: B 7 PRO cc_start: 0.7540 (Cg_endo) cc_final: 0.7288 (Cg_exo) REVERT: B 70 SER cc_start: 0.7598 (t) cc_final: 0.7088 (m) REVERT: B 154 MET cc_start: 0.8128 (mtt) cc_final: 0.7817 (mtt) REVERT: B 156 TRP cc_start: 0.8697 (m-90) cc_final: 0.8357 (m-90) REVERT: C 72 GLN cc_start: 0.7731 (pm20) cc_final: 0.6720 (mt0) REVERT: C 81 ILE cc_start: 0.7586 (mm) cc_final: 0.7346 (mm) REVERT: C 190 PHE cc_start: 0.8061 (t80) cc_final: 0.7708 (t80) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1567 time to fit residues: 26.2728 Evaluate side-chains 103 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 6.9990 chunk 10 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 70 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.159317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.146440 restraints weight = 29196.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.146236 restraints weight = 32120.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.143630 restraints weight = 12047.340| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6564 Z= 0.197 Angle : 0.636 7.814 8989 Z= 0.304 Chirality : 0.042 0.271 1070 Planarity : 0.005 0.053 1105 Dihedral : 8.721 98.182 1416 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.19 % Allowed : 0.75 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.29), residues: 862 helix: 1.73 (0.27), residues: 374 sheet: -0.03 (0.39), residues: 175 loop : -2.03 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 46 HIS 0.000 0.000 HIS A 156 PHE 0.032 0.002 PHE A 431 TYR 0.025 0.001 TYR A 358 ARG 0.007 0.001 ARG B 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1755.05 seconds wall clock time: 32 minutes 38.99 seconds (1958.99 seconds total)