Starting phenix.real_space_refine on Fri Dec 27 08:50:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6q_50238/12_2024/9f6q_50238.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6q_50238/12_2024/9f6q_50238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f6q_50238/12_2024/9f6q_50238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6q_50238/12_2024/9f6q_50238.map" model { file = "/net/cci-nas-00/data/ceres_data/9f6q_50238/12_2024/9f6q_50238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6q_50238/12_2024/9f6q_50238.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 2392 2.51 5 N 589 2.21 5 O 615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3618 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3618 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 19, 'TRANS': 449} Time building chain proxies: 2.79, per 1000 atoms: 0.77 Number of scatterers: 3618 At special positions: 0 Unit cell: (84.63, 69.006, 71.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 615 8.00 N 589 7.00 C 2392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 354 " 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 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 460.7 milliseconds 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 864 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 87.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 54 through 62 Processing helix chain 'A' and resid 63 through 73 removed outlier: 3.887A pdb=" N LEU A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 88 Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 92 through 118 Processing helix chain 'A' and resid 120 through 129 Processing helix chain 'A' and resid 130 through 165 Processing helix chain 'A' and resid 169 through 187 Processing helix chain 'A' and resid 188 through 191 removed outlier: 3.747A pdb=" N GLY A 191 " --> pdb=" O ASP A 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 188 through 191' Processing helix chain 'A' and resid 195 through 218 Processing helix chain 'A' and resid 220 through 230 removed outlier: 4.182A pdb=" N LEU A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 252 removed outlier: 3.733A pdb=" N ILE A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 removed outlier: 4.517A pdb=" N TYR A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 273 through 311 removed outlier: 3.525A pdb=" N ILE A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'A' and resid 344 through 357 Processing helix chain 'A' and resid 357 through 391 removed outlier: 3.756A pdb=" N LEU A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 419 Proline residue: A 411 - end of helix Processing helix chain 'A' and resid 420 through 439 Processing helix chain 'A' and resid 439 through 452 Proline residue: A 445 - end of helix removed outlier: 3.557A pdb=" N MET A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 488 Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 495 through 522 removed outlier: 4.521A pdb=" N LEU A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) 302 hydrogen bonds defined for protein. 906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1121 1.34 - 1.46: 905 1.46 - 1.58: 1646 1.58 - 1.70: 0 1.70 - 1.82: 34 Bond restraints: 3706 Sorted by residual: bond pdb=" N LEU A 361 " pdb=" CA LEU A 361 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.20e-02 6.94e+03 4.32e+00 bond pdb=" CG1 ILE A 141 " pdb=" CD1 ILE A 141 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.93e+00 bond pdb=" CG MET A 68 " pdb=" SD MET A 68 " ideal model delta sigma weight residual 1.803 1.771 0.032 2.50e-02 1.60e+03 1.61e+00 bond pdb=" CB GLU A 268 " pdb=" CG GLU A 268 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CB PRO A 335 " pdb=" CG PRO A 335 " ideal model delta sigma weight residual 1.492 1.543 -0.051 5.00e-02 4.00e+02 1.04e+00 ... (remaining 3701 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 4849 1.72 - 3.45: 149 3.45 - 5.17: 31 5.17 - 6.89: 14 6.89 - 8.61: 10 Bond angle restraints: 5053 Sorted by residual: angle pdb=" CA MET A 68 " pdb=" CB MET A 68 " pdb=" CG MET A 68 " ideal model delta sigma weight residual 114.10 121.17 -7.07 2.00e+00 2.50e-01 1.25e+01 angle pdb=" N ILE A 141 " pdb=" CA ILE A 141 " pdb=" CB ILE A 141 " ideal model delta sigma weight residual 110.65 116.54 -5.89 1.71e+00 3.42e-01 1.19e+01 angle pdb=" N MET A 68 " pdb=" CA MET A 68 " pdb=" CB MET A 68 " ideal model delta sigma weight residual 110.16 114.90 -4.74 1.48e+00 4.57e-01 1.03e+01 angle pdb=" CA MET A 473 " pdb=" CB MET A 473 " pdb=" CG MET A 473 " ideal model delta sigma weight residual 114.10 120.43 -6.33 2.00e+00 2.50e-01 1.00e+01 angle pdb=" CA ILE A 141 " pdb=" CB ILE A 141 " pdb=" CG1 ILE A 141 " ideal model delta sigma weight residual 110.40 115.68 -5.28 1.70e+00 3.46e-01 9.66e+00 ... (remaining 5048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 1830 15.99 - 31.98: 233 31.98 - 47.97: 75 47.97 - 63.96: 14 63.96 - 79.95: 5 Dihedral angle restraints: 2157 sinusoidal: 808 harmonic: 1349 Sorted by residual: dihedral pdb=" CB CYS A 233 " pdb=" SG CYS A 233 " pdb=" SG CYS A 236 " pdb=" CB CYS A 236 " ideal model delta sinusoidal sigma weight residual 93.00 166.71 -73.71 1 1.00e+01 1.00e-02 6.91e+01 dihedral pdb=" CB CYS A 322 " pdb=" SG CYS A 322 " pdb=" SG CYS A 354 " pdb=" CB CYS A 354 " ideal model delta sinusoidal sigma weight residual -86.00 -45.81 -40.19 1 1.00e+01 1.00e-02 2.27e+01 dihedral pdb=" CA PHE A 334 " pdb=" C PHE A 334 " pdb=" N PRO A 335 " pdb=" CA PRO A 335 " ideal model delta harmonic sigma weight residual 180.00 162.04 17.96 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 2154 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 407 0.037 - 0.075: 133 0.075 - 0.112: 48 0.112 - 0.150: 12 0.150 - 0.187: 2 Chirality restraints: 602 Sorted by residual: chirality pdb=" CB THR A 209 " pdb=" CA THR A 209 " pdb=" OG1 THR A 209 " pdb=" CG2 THR A 209 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CB THR A 412 " pdb=" CA THR A 412 " pdb=" OG1 THR A 412 " pdb=" CG2 THR A 412 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.00e-01 chirality pdb=" CA MET A 68 " pdb=" N MET A 68 " pdb=" C MET A 68 " pdb=" CB MET A 68 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 599 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 63 " -0.033 5.00e-02 4.00e+02 5.06e-02 4.09e+00 pdb=" N PRO A 64 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 296 " -0.006 2.00e-02 2.50e+03 1.42e-02 3.52e+00 pdb=" CG PHE A 296 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 296 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 296 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 296 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 296 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 296 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 230 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO A 231 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " -0.022 5.00e-02 4.00e+02 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 568 2.76 - 3.29: 3996 3.29 - 3.83: 6369 3.83 - 4.36: 6782 4.36 - 4.90: 11324 Nonbonded interactions: 29039 Sorted by model distance: nonbonded pdb=" O LEU A 58 " pdb=" OG1 THR A 62 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR A 450 " pdb=" OD1 ASN A 461 " model vdw 2.245 3.040 nonbonded pdb=" O GLY A 372 " pdb=" OG1 THR A 376 " model vdw 2.312 3.040 nonbonded pdb=" O MET A 377 " pdb=" OG1 THR A 380 " model vdw 2.322 3.040 nonbonded pdb=" OE2 GLU A 142 " pdb=" NH2 ARG A 400 " model vdw 2.334 3.120 ... (remaining 29034 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=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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.660 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 3706 Z= 0.226 Angle : 0.826 8.612 5053 Z= 0.414 Chirality : 0.044 0.187 602 Planarity : 0.005 0.051 624 Dihedral : 15.985 79.954 1287 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.62 % Allowed : 23.10 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.40), residues: 467 helix: 1.47 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -1.83 (0.67), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 94 HIS 0.004 0.001 HIS A 493 PHE 0.030 0.002 PHE A 296 TYR 0.017 0.001 TYR A 362 ARG 0.005 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.8201 (m-10) cc_final: 0.7573 (m-10) REVERT: A 120 ASP cc_start: 0.7306 (p0) cc_final: 0.6729 (p0) REVERT: A 138 TRP cc_start: 0.8426 (t60) cc_final: 0.7959 (t60) REVERT: A 167 ARG cc_start: 0.5113 (mtt90) cc_final: 0.4650 (tpt170) REVERT: A 268 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8208 (mp0) REVERT: A 297 ILE cc_start: 0.9518 (pt) cc_final: 0.8929 (pt) REVERT: A 319 PHE cc_start: 0.7102 (t80) cc_final: 0.6724 (t80) REVERT: A 346 TYR cc_start: 0.7927 (t80) cc_final: 0.7288 (t80) REVERT: A 384 GLN cc_start: 0.8102 (tt0) cc_final: 0.7852 (tm-30) REVERT: A 394 ARG cc_start: 0.7880 (tpt-90) cc_final: 0.7209 (tpt90) outliers start: 10 outliers final: 5 residues processed: 163 average time/residue: 0.1352 time to fit residues: 27.8193 Evaluate side-chains 142 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.8980 chunk 34 optimal weight: 0.0270 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.0010 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.4844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3706 Z= 0.206 Angle : 0.809 9.307 5053 Z= 0.413 Chirality : 0.046 0.180 602 Planarity : 0.006 0.058 624 Dihedral : 5.971 50.234 515 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.67 % Allowed : 26.51 % Favored : 69.82 % 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: 1.45 (0.40), residues: 467 helix: 1.56 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.52 (0.67), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 364 HIS 0.003 0.001 HIS A 493 PHE 0.031 0.002 PHE A 199 TYR 0.021 0.002 TYR A 362 ARG 0.002 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.8079 (m-10) cc_final: 0.7509 (m-80) REVERT: A 70 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8739 (mp) REVERT: A 139 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9139 (mm) REVERT: A 142 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8257 (mm-30) REVERT: A 265 LYS cc_start: 0.8237 (mttp) cc_final: 0.7969 (mptt) REVERT: A 268 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8143 (mp0) REVERT: A 297 ILE cc_start: 0.9411 (pt) cc_final: 0.9063 (pt) REVERT: A 384 GLN cc_start: 0.8049 (tt0) cc_final: 0.7648 (tm-30) REVERT: A 456 MET cc_start: 0.7200 (mpp) cc_final: 0.6869 (mpp) REVERT: A 514 LEU cc_start: 0.9149 (mm) cc_final: 0.8887 (mm) outliers start: 14 outliers final: 9 residues processed: 149 average time/residue: 0.1141 time to fit residues: 22.2758 Evaluate side-chains 144 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 41 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3706 Z= 0.205 Angle : 0.799 10.682 5053 Z= 0.400 Chirality : 0.045 0.165 602 Planarity : 0.006 0.059 624 Dihedral : 5.681 50.304 511 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 6.30 % Allowed : 26.77 % Favored : 66.93 % 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: 1.55 (0.40), residues: 467 helix: 1.62 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.42 (0.67), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 138 HIS 0.004 0.001 HIS A 255 PHE 0.041 0.002 PHE A 301 TYR 0.020 0.001 TYR A 362 ARG 0.003 0.000 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 66 PHE cc_start: 0.8097 (m-10) cc_final: 0.7552 (m-80) REVERT: A 70 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8785 (mp) REVERT: A 138 TRP cc_start: 0.8154 (t60) cc_final: 0.7874 (t60) REVERT: A 142 GLU cc_start: 0.8593 (mm-30) cc_final: 0.7978 (mm-30) REVERT: A 167 ARG cc_start: 0.4901 (mtt180) cc_final: 0.3732 (tpt170) REVERT: A 192 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6244 (mp) REVERT: A 255 HIS cc_start: 0.8854 (p90) cc_final: 0.8609 (p90) REVERT: A 268 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8118 (mp0) REVERT: A 297 ILE cc_start: 0.9435 (pt) cc_final: 0.9217 (pt) REVERT: A 384 GLN cc_start: 0.7986 (tt0) cc_final: 0.7733 (tm-30) outliers start: 24 outliers final: 13 residues processed: 146 average time/residue: 0.1185 time to fit residues: 22.1574 Evaluate side-chains 140 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 0.0470 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 0.0070 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3706 Z= 0.201 Angle : 0.848 12.083 5053 Z= 0.413 Chirality : 0.047 0.275 602 Planarity : 0.006 0.058 624 Dihedral : 5.772 50.077 511 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.51 % Allowed : 28.08 % Favored : 66.40 % 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: 1.58 (0.39), residues: 467 helix: 1.66 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -1.40 (0.64), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 138 HIS 0.002 0.001 HIS A 255 PHE 0.042 0.002 PHE A 301 TYR 0.028 0.001 TYR A 362 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.8077 (m-10) cc_final: 0.7523 (m-80) REVERT: A 70 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8775 (mp) REVERT: A 138 TRP cc_start: 0.8177 (t60) cc_final: 0.7942 (t60) REVERT: A 142 GLU cc_start: 0.8678 (mm-30) cc_final: 0.7923 (mm-30) REVERT: A 167 ARG cc_start: 0.5208 (mtt180) cc_final: 0.3455 (tpt170) REVERT: A 192 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6113 (mp) REVERT: A 255 HIS cc_start: 0.8865 (p90) cc_final: 0.8608 (p90) REVERT: A 265 LYS cc_start: 0.8529 (mttp) cc_final: 0.8201 (mptt) REVERT: A 268 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8129 (mp0) REVERT: A 384 GLN cc_start: 0.8027 (tt0) cc_final: 0.7723 (tm-30) outliers start: 21 outliers final: 14 residues processed: 152 average time/residue: 0.1142 time to fit residues: 22.6626 Evaluate side-chains 144 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.0030 chunk 18 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3706 Z= 0.211 Angle : 0.879 12.346 5053 Z= 0.426 Chirality : 0.049 0.331 602 Planarity : 0.006 0.058 624 Dihedral : 5.800 49.815 511 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 6.04 % Allowed : 30.97 % Favored : 62.99 % 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: 1.50 (0.39), residues: 467 helix: 1.58 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -1.36 (0.64), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 138 HIS 0.002 0.001 HIS A 328 PHE 0.046 0.002 PHE A 301 TYR 0.024 0.001 TYR A 362 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.8075 (m-10) cc_final: 0.7535 (m-80) REVERT: A 142 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8022 (mm-30) REVERT: A 167 ARG cc_start: 0.5235 (mtt180) cc_final: 0.3562 (tpt170) REVERT: A 192 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6010 (mp) REVERT: A 265 LYS cc_start: 0.8473 (mttp) cc_final: 0.8126 (mptt) REVERT: A 268 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8150 (mp0) REVERT: A 384 GLN cc_start: 0.7868 (tt0) cc_final: 0.7627 (tm-30) outliers start: 23 outliers final: 13 residues processed: 148 average time/residue: 0.1054 time to fit residues: 20.5249 Evaluate side-chains 145 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3706 Z= 0.235 Angle : 0.893 13.140 5053 Z= 0.437 Chirality : 0.050 0.319 602 Planarity : 0.006 0.060 624 Dihedral : 5.869 48.595 511 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 6.56 % Allowed : 32.81 % Favored : 60.63 % 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: 1.44 (0.39), residues: 467 helix: 1.51 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.33 (0.65), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 138 HIS 0.002 0.001 HIS A 255 PHE 0.044 0.002 PHE A 301 TYR 0.024 0.002 TYR A 362 ARG 0.002 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 66 PHE cc_start: 0.8202 (m-10) cc_final: 0.7963 (m-10) REVERT: A 142 GLU cc_start: 0.8617 (mm-30) cc_final: 0.7950 (mm-30) REVERT: A 192 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6147 (mp) REVERT: A 229 PHE cc_start: 0.6590 (t80) cc_final: 0.6110 (t80) REVERT: A 265 LYS cc_start: 0.8307 (mttp) cc_final: 0.7999 (mptt) REVERT: A 268 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8156 (mp0) REVERT: A 387 MET cc_start: 0.7601 (mmt) cc_final: 0.7152 (mpp) REVERT: A 443 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8755 (p) outliers start: 25 outliers final: 15 residues processed: 153 average time/residue: 0.1150 time to fit residues: 22.9748 Evaluate side-chains 148 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.0570 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3706 Z= 0.250 Angle : 0.939 13.573 5053 Z= 0.459 Chirality : 0.051 0.318 602 Planarity : 0.006 0.062 624 Dihedral : 6.010 50.147 511 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 6.30 % Allowed : 34.65 % Favored : 59.06 % 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: 1.29 (0.39), residues: 467 helix: 1.44 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -1.45 (0.65), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 138 HIS 0.004 0.001 HIS A 328 PHE 0.045 0.002 PHE A 301 TYR 0.030 0.002 TYR A 362 ARG 0.005 0.001 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 66 PHE cc_start: 0.8178 (m-10) cc_final: 0.7732 (m-10) REVERT: A 192 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.5997 (mp) REVERT: A 229 PHE cc_start: 0.6489 (t80) cc_final: 0.5998 (t80) REVERT: A 268 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8153 (mp0) outliers start: 24 outliers final: 16 residues processed: 144 average time/residue: 0.1085 time to fit residues: 20.4230 Evaluate side-chains 148 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 0.0370 chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 3706 Z= 0.246 Angle : 1.018 16.667 5053 Z= 0.483 Chirality : 0.053 0.317 602 Planarity : 0.006 0.062 624 Dihedral : 6.087 53.473 511 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.51 % Allowed : 35.96 % Favored : 58.53 % 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: 1.19 (0.39), residues: 467 helix: 1.34 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -1.53 (0.66), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 138 HIS 0.003 0.001 HIS A 255 PHE 0.051 0.002 PHE A 301 TYR 0.028 0.002 TYR A 362 ARG 0.002 0.000 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.5718 (mp) REVERT: A 229 PHE cc_start: 0.6316 (t80) cc_final: 0.5778 (t80) REVERT: A 268 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8165 (mp0) REVERT: A 364 TRP cc_start: 0.8700 (t60) cc_final: 0.8469 (t60) outliers start: 21 outliers final: 17 residues processed: 143 average time/residue: 0.1198 time to fit residues: 22.1150 Evaluate side-chains 149 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 HIS ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3706 Z= 0.285 Angle : 1.029 15.071 5053 Z= 0.504 Chirality : 0.054 0.274 602 Planarity : 0.006 0.062 624 Dihedral : 6.257 53.220 511 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.77 % Allowed : 35.70 % Favored : 58.53 % 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: 1.11 (0.39), residues: 467 helix: 1.29 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -1.38 (0.63), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 138 HIS 0.004 0.001 HIS A 328 PHE 0.053 0.003 PHE A 186 TYR 0.027 0.002 TYR A 362 ARG 0.003 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7102 (pm20) REVERT: A 167 ARG cc_start: 0.4845 (mtt180) cc_final: 0.3360 (tpt170) REVERT: A 192 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.5883 (mp) REVERT: A 229 PHE cc_start: 0.6297 (t80) cc_final: 0.5686 (t80) REVERT: A 364 TRP cc_start: 0.8824 (t60) cc_final: 0.8580 (t60) REVERT: A 384 GLN cc_start: 0.8112 (tt0) cc_final: 0.7249 (pt0) outliers start: 22 outliers final: 19 residues processed: 141 average time/residue: 0.1109 time to fit residues: 20.4654 Evaluate side-chains 151 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 0.0770 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 HIS ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 3706 Z= 0.259 Angle : 1.044 15.017 5053 Z= 0.508 Chirality : 0.055 0.316 602 Planarity : 0.006 0.062 624 Dihedral : 6.254 56.161 511 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 5.51 % Allowed : 37.80 % Favored : 56.69 % 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: 1.12 (0.39), residues: 467 helix: 1.32 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -1.49 (0.65), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 138 HIS 0.003 0.001 HIS A 328 PHE 0.054 0.003 PHE A 301 TYR 0.027 0.002 TYR A 362 ARG 0.007 0.001 ARG A 267 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6959 (pm20) REVERT: A 167 ARG cc_start: 0.4889 (mtt180) cc_final: 0.3363 (tpt170) REVERT: A 192 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.5800 (mp) REVERT: A 229 PHE cc_start: 0.6359 (t80) cc_final: 0.5797 (t80) REVERT: A 336 MET cc_start: 0.7250 (mmm) cc_final: 0.6937 (mmp) REVERT: A 364 TRP cc_start: 0.8804 (t60) cc_final: 0.8558 (t60) REVERT: A 384 GLN cc_start: 0.8215 (tt0) cc_final: 0.7364 (pt0) outliers start: 21 outliers final: 18 residues processed: 143 average time/residue: 0.1107 time to fit residues: 20.7855 Evaluate side-chains 151 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 HIS ** A 435 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 = 0.3880 r_free = 0.3880 target = 0.117841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.099954 restraints weight = 11286.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.102622 restraints weight = 7674.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.104712 restraints weight = 5653.971| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3706 Z= 0.262 Angle : 1.052 15.365 5053 Z= 0.512 Chirality : 0.055 0.305 602 Planarity : 0.006 0.062 624 Dihedral : 5.960 56.841 509 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.77 % Allowed : 36.48 % Favored : 57.74 % 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: 1.03 (0.39), residues: 467 helix: 1.21 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -1.47 (0.66), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 138 HIS 0.003 0.001 HIS A 328 PHE 0.055 0.003 PHE A 301 TYR 0.026 0.002 TYR A 362 ARG 0.006 0.001 ARG A 267 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1129.52 seconds wall clock time: 21 minutes 11.93 seconds (1271.93 seconds total)