Starting phenix.real_space_refine on Sun Mar 10 20:27:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr5_34046/03_2024/7yr5_34046.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr5_34046/03_2024/7yr5_34046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr5_34046/03_2024/7yr5_34046.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr5_34046/03_2024/7yr5_34046.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr5_34046/03_2024/7yr5_34046.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr5_34046/03_2024/7yr5_34046.pdb" } resolution = 3.63 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= -0.000 sd= 0.015 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 35 5.16 5 C 3164 2.51 5 N 775 2.21 5 O 854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 79": "OE1" <-> "OE2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 438": "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: 4828 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1899 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain: "A" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2929 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 367} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 3.26, per 1000 atoms: 0.68 Number of scatterers: 4828 At special positions: 0 Unit cell: (73.08, 103.32, 123.48, 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 35 16.00 O 854 8.00 N 775 7.00 C 3164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 88 " - pdb=" SG CYS B 142 " distance=2.04 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 237 " 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: 2.23 Conformation dependent library (CDL) restraints added in 928.6 milliseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1126 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 5 sheets defined 61.7% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'B' and resid 257 through 290 removed outlier: 4.103A pdb=" N LYS B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Proline residue: B 263 - end of helix Processing helix chain 'A' and resid 19 through 40 removed outlier: 4.237A pdb=" N PHE A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Proline residue: A 37 - end of helix Processing helix chain 'A' and resid 40 through 51 removed outlier: 4.150A pdb=" N LYS A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 72 removed outlier: 5.085A pdb=" N ILE A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 83 Processing helix chain 'A' and resid 84 through 104 Processing helix chain 'A' and resid 111 through 139 removed outlier: 3.690A pdb=" N CYS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 142 through 152 Processing helix chain 'A' and resid 152 through 162 removed outlier: 4.313A pdb=" N VAL A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 172 removed outlier: 5.924A pdb=" N PHE A 169 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 188 removed outlier: 3.519A pdb=" N ILE A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.551A pdb=" N LEU A 257 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 291 removed outlier: 4.491A pdb=" N PHE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLY A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Proline residue: A 280 - end of helix removed outlier: 5.279A pdb=" N SER A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N SER A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 322 removed outlier: 3.590A pdb=" N LEU A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Proline residue: A 314 - end of helix Processing helix chain 'A' and resid 323 through 326 Processing helix chain 'A' and resid 328 through 347 removed outlier: 3.607A pdb=" N VAL A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 339 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A 340 " --> pdb=" O SER A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 374 removed outlier: 3.859A pdb=" N TRP A 369 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 382 Processing helix chain 'A' and resid 383 through 412 removed outlier: 3.983A pdb=" N SER A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N SER A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N CYS A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) Proline residue: A 401 - end of helix Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 421 through 448 removed outlier: 3.934A pdb=" N ALA A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS A 426 " --> pdb=" O THR A 422 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 61 through 64 removed outlier: 5.621A pdb=" N ILE B 62 " --> pdb=" O GLN B 89 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N THR B 91 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU B 64 " --> pdb=" O THR B 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 72 through 74 removed outlier: 3.715A pdb=" N GLN B 150 " --> pdb=" O PHE B 144 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TRP B 103 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 169 through 171 Processing sheet with id=AA4, first strand: chain 'B' and resid 191 through 194 Processing sheet with id=AA5, first strand: chain 'B' and resid 210 through 213 278 hydrogen bonds defined for protein. 798 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: 1.39 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1472 1.34 - 1.46: 1090 1.46 - 1.58: 2336 1.58 - 1.70: 0 1.70 - 1.81: 51 Bond restraints: 4949 Sorted by residual: bond pdb=" N VAL B 84 " pdb=" CA VAL B 84 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.11e-02 8.12e+03 1.16e+01 bond pdb=" N ILE B 76 " pdb=" CA ILE B 76 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.19e-02 7.06e+03 9.69e+00 bond pdb=" N VAL B 116 " pdb=" CA VAL B 116 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.22e-02 6.72e+03 8.68e+00 bond pdb=" N VAL B 72 " pdb=" CA VAL B 72 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.24e-02 6.50e+03 8.36e+00 bond pdb=" N LYS B 104 " pdb=" CA LYS B 104 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.27e-02 6.20e+03 7.61e+00 ... (remaining 4944 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.08: 110 106.08 - 113.13: 2604 113.13 - 120.18: 1927 120.18 - 127.23: 2022 127.23 - 134.28: 52 Bond angle restraints: 6715 Sorted by residual: angle pdb=" C ARG B 128 " pdb=" N PHE B 129 " pdb=" CA PHE B 129 " ideal model delta sigma weight residual 122.77 117.48 5.29 1.33e+00 5.65e-01 1.58e+01 angle pdb=" CA PHE B 129 " pdb=" CB PHE B 129 " pdb=" CG PHE B 129 " ideal model delta sigma weight residual 113.80 117.77 -3.97 1.00e+00 1.00e+00 1.58e+01 angle pdb=" N PHE B 154 " pdb=" CA PHE B 154 " pdb=" C PHE B 154 " ideal model delta sigma weight residual 109.46 103.18 6.28 1.66e+00 3.63e-01 1.43e+01 angle pdb=" C CYS A 106 " pdb=" N ASN A 107 " pdb=" CA ASN A 107 " ideal model delta sigma weight residual 122.61 128.02 -5.41 1.56e+00 4.11e-01 1.20e+01 angle pdb=" C CYS B 88 " pdb=" N GLN B 89 " pdb=" CA GLN B 89 " ideal model delta sigma weight residual 123.05 118.23 4.82 1.40e+00 5.10e-01 1.18e+01 ... (remaining 6710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.54: 2481 14.54 - 29.07: 292 29.07 - 43.61: 82 43.61 - 58.14: 13 58.14 - 72.68: 7 Dihedral angle restraints: 2875 sinusoidal: 1101 harmonic: 1774 Sorted by residual: dihedral pdb=" CA GLN A 166 " pdb=" C GLN A 166 " pdb=" N VAL A 167 " pdb=" CA VAL A 167 " ideal model delta harmonic sigma weight residual 180.00 153.92 26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA LEU A 164 " pdb=" C LEU A 164 " pdb=" N ASN A 165 " pdb=" CA ASN A 165 " ideal model delta harmonic sigma weight residual 180.00 158.35 21.65 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLN A 110 " pdb=" C GLN A 110 " pdb=" N GLN A 111 " pdb=" CA GLN A 111 " ideal model delta harmonic sigma weight residual 180.00 159.98 20.02 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 2872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 571 0.052 - 0.104: 141 0.104 - 0.156: 34 0.156 - 0.208: 12 0.208 - 0.261: 4 Chirality restraints: 762 Sorted by residual: chirality pdb=" CA PHE B 154 " pdb=" N PHE B 154 " pdb=" C PHE B 154 " pdb=" CB PHE B 154 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA CYS B 88 " pdb=" N CYS B 88 " pdb=" C CYS B 88 " pdb=" CB CYS B 88 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE B 62 " pdb=" N ILE B 62 " pdb=" C ILE B 62 " pdb=" CB ILE B 62 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 759 not shown) Planarity restraints: 834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 253 " 0.021 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C VAL B 253 " -0.073 2.00e-02 2.50e+03 pdb=" O VAL B 253 " 0.027 2.00e-02 2.50e+03 pdb=" N VAL B 254 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 99 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C VAL B 99 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL B 99 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN B 100 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 114 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" C VAL A 114 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL A 114 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS A 115 " -0.011 2.00e-02 2.50e+03 ... (remaining 831 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1062 2.78 - 3.31: 4795 3.31 - 3.84: 7906 3.84 - 4.37: 9100 4.37 - 4.90: 15390 Nonbonded interactions: 38253 Sorted by model distance: nonbonded pdb=" OG SER A 63 " pdb=" O LEU A 403 " model vdw 2.250 2.440 nonbonded pdb=" OG SER A 29 " pdb=" O ASN A 127 " model vdw 2.276 2.440 nonbonded pdb=" OH TYR A 138 " pdb=" O ARG A 196 " model vdw 2.290 2.440 nonbonded pdb=" OH TYR B 210 " pdb=" OH TYR B 235 " model vdw 2.292 2.440 nonbonded pdb=" OG SER B 134 " pdb=" O GLU B 160 " model vdw 2.318 2.440 ... (remaining 38248 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.760 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.670 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4949 Z= 0.326 Angle : 0.808 6.881 6715 Z= 0.501 Chirality : 0.054 0.261 762 Planarity : 0.005 0.042 834 Dihedral : 13.919 72.678 1743 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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 (0.34), residues: 616 helix: 0.65 (0.29), residues: 362 sheet: 0.32 (0.53), residues: 102 loop : -1.81 (0.42), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 236 HIS 0.002 0.000 HIS B 249 PHE 0.017 0.001 PHE B 129 TYR 0.013 0.001 TYR A 445 ARG 0.003 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.425 Fit side-chains REVERT: A 151 MET cc_start: 0.8056 (ttm) cc_final: 0.7434 (ttp) REVERT: A 416 TYR cc_start: 0.7273 (t80) cc_final: 0.6929 (t80) REVERT: A 418 ASP cc_start: 0.7536 (t70) cc_final: 0.7060 (p0) REVERT: A 446 ARG cc_start: 0.8201 (mmp80) cc_final: 0.7579 (mtp180) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1476 time to fit residues: 21.8365 Evaluate side-chains 84 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN A 165 ASN A 260 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4949 Z= 0.327 Angle : 0.681 10.751 6715 Z= 0.358 Chirality : 0.045 0.148 762 Planarity : 0.005 0.046 834 Dihedral : 5.110 26.151 665 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.23 % Allowed : 13.47 % Favored : 83.30 % 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: 0.00 (0.34), residues: 616 helix: 0.66 (0.28), residues: 365 sheet: 0.13 (0.53), residues: 100 loop : -1.53 (0.44), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 369 HIS 0.006 0.001 HIS A 260 PHE 0.018 0.002 PHE B 129 TYR 0.011 0.001 TYR A 445 ARG 0.002 0.000 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.592 Fit side-chains REVERT: A 48 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7417 (mm-30) REVERT: A 83 TYR cc_start: 0.6962 (m-10) cc_final: 0.6693 (m-10) REVERT: A 418 ASP cc_start: 0.7615 (t70) cc_final: 0.7226 (p0) REVERT: A 438 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7751 (t80) outliers start: 17 outliers final: 11 residues processed: 97 average time/residue: 0.1235 time to fit residues: 16.6033 Evaluate side-chains 93 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 438 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN A 127 ASN A 129 ASN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4949 Z= 0.226 Angle : 0.617 8.880 6715 Z= 0.321 Chirality : 0.042 0.134 762 Planarity : 0.005 0.044 834 Dihedral : 4.914 22.288 665 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.04 % Allowed : 19.35 % Favored : 77.61 % 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: 0.14 (0.35), residues: 616 helix: 0.84 (0.29), residues: 362 sheet: 0.06 (0.54), residues: 104 loop : -1.57 (0.45), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 236 HIS 0.003 0.001 HIS B 249 PHE 0.015 0.001 PHE B 129 TYR 0.009 0.001 TYR B 124 ARG 0.001 0.000 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.596 Fit side-chains REVERT: A 48 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7319 (mm-30) REVERT: A 82 LYS cc_start: 0.8287 (ttpp) cc_final: 0.7322 (tmmt) REVERT: A 416 TYR cc_start: 0.7621 (t80) cc_final: 0.7043 (t80) REVERT: A 420 LYS cc_start: 0.9042 (tmmt) cc_final: 0.8312 (ttpp) REVERT: A 438 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7703 (t80) outliers start: 16 outliers final: 11 residues processed: 100 average time/residue: 0.1362 time to fit residues: 18.4618 Evaluate side-chains 99 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 438 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 4949 Z= 0.450 Angle : 0.758 9.005 6715 Z= 0.399 Chirality : 0.047 0.166 762 Planarity : 0.005 0.047 834 Dihedral : 5.405 27.844 665 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.98 % Allowed : 23.15 % Favored : 72.87 % 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: -0.30 (0.34), residues: 616 helix: 0.40 (0.28), residues: 367 sheet: 0.03 (0.55), residues: 100 loop : -1.61 (0.46), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 369 HIS 0.005 0.001 HIS B 249 PHE 0.018 0.002 PHE B 129 TYR 0.014 0.002 TYR A 140 ARG 0.002 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 0.542 Fit side-chains outliers start: 21 outliers final: 15 residues processed: 102 average time/residue: 0.1288 time to fit residues: 18.0238 Evaluate side-chains 91 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 372 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN A 129 ASN A 166 GLN A 291 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4949 Z= 0.222 Angle : 0.615 8.047 6715 Z= 0.321 Chirality : 0.042 0.134 762 Planarity : 0.005 0.046 834 Dihedral : 5.057 24.696 665 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.55 % Allowed : 23.72 % Favored : 71.73 % 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 (0.35), residues: 616 helix: 0.71 (0.28), residues: 368 sheet: 0.01 (0.55), residues: 100 loop : -1.45 (0.46), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 236 HIS 0.004 0.001 HIS B 249 PHE 0.015 0.002 PHE B 129 TYR 0.010 0.001 TYR A 287 ARG 0.001 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 0.495 Fit side-chains REVERT: A 48 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7402 (mm-30) REVERT: A 374 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8832 (tt) REVERT: A 420 LYS cc_start: 0.9003 (tmmt) cc_final: 0.8424 (ttpp) REVERT: A 438 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7651 (t80) outliers start: 24 outliers final: 17 residues processed: 104 average time/residue: 0.1326 time to fit residues: 18.7601 Evaluate side-chains 105 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 278 PHE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 438 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4949 Z= 0.253 Angle : 0.631 9.381 6715 Z= 0.330 Chirality : 0.043 0.141 762 Planarity : 0.005 0.044 834 Dihedral : 5.047 26.034 665 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 4.74 % Allowed : 25.43 % Favored : 69.83 % 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 (0.35), residues: 616 helix: 0.74 (0.29), residues: 368 sheet: -0.07 (0.55), residues: 101 loop : -1.49 (0.46), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 236 HIS 0.004 0.001 HIS B 249 PHE 0.018 0.002 PHE A 307 TYR 0.009 0.001 TYR B 210 ARG 0.001 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 0.551 Fit side-chains REVERT: A 48 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7358 (mm-30) REVERT: A 374 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8828 (tt) REVERT: A 420 LYS cc_start: 0.8974 (tmmt) cc_final: 0.8331 (ttpp) REVERT: A 438 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7684 (t80) outliers start: 25 outliers final: 19 residues processed: 104 average time/residue: 0.1313 time to fit residues: 18.5941 Evaluate side-chains 105 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 278 PHE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 438 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN A 129 ASN A 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4949 Z= 0.289 Angle : 0.656 9.849 6715 Z= 0.343 Chirality : 0.043 0.144 762 Planarity : 0.005 0.044 834 Dihedral : 5.122 26.425 665 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 4.93 % Allowed : 26.19 % Favored : 68.88 % 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: 0.00 (0.35), residues: 616 helix: 0.72 (0.28), residues: 368 sheet: -0.13 (0.55), residues: 101 loop : -1.53 (0.46), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 236 HIS 0.004 0.001 HIS B 249 PHE 0.015 0.002 PHE B 129 TYR 0.009 0.001 TYR B 210 ARG 0.002 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 88 time to evaluate : 0.558 Fit side-chains REVERT: B 88 CYS cc_start: 0.1822 (OUTLIER) cc_final: 0.1048 (t) REVERT: A 48 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7457 (mm-30) REVERT: A 65 MET cc_start: 0.8604 (tpp) cc_final: 0.8213 (ttm) REVERT: A 374 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8770 (tt) REVERT: A 438 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7695 (t80) outliers start: 26 outliers final: 18 residues processed: 105 average time/residue: 0.1405 time to fit residues: 20.5434 Evaluate side-chains 105 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 278 PHE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 438 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 53 optimal weight: 0.0980 chunk 56 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 54 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN A 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4949 Z= 0.189 Angle : 0.603 8.413 6715 Z= 0.315 Chirality : 0.041 0.133 762 Planarity : 0.005 0.044 834 Dihedral : 4.934 25.232 665 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.04 % Allowed : 28.27 % Favored : 68.69 % 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: 0.20 (0.35), residues: 616 helix: 0.95 (0.29), residues: 362 sheet: -0.02 (0.56), residues: 101 loop : -1.61 (0.44), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 236 HIS 0.003 0.001 HIS B 249 PHE 0.022 0.002 PHE A 307 TYR 0.007 0.001 TYR A 353 ARG 0.001 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.556 Fit side-chains REVERT: A 65 MET cc_start: 0.8488 (tpp) cc_final: 0.8239 (ttm) REVERT: A 438 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7678 (t80) outliers start: 16 outliers final: 14 residues processed: 98 average time/residue: 0.1364 time to fit residues: 18.2271 Evaluate side-chains 100 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 PHE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 438 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN A 129 ASN A 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4949 Z= 0.307 Angle : 0.677 9.640 6715 Z= 0.352 Chirality : 0.044 0.149 762 Planarity : 0.005 0.043 834 Dihedral : 5.120 26.827 665 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.55 % Allowed : 27.13 % Favored : 68.31 % 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: 0.03 (0.35), residues: 616 helix: 0.79 (0.29), residues: 368 sheet: -0.18 (0.55), residues: 101 loop : -1.63 (0.45), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 369 HIS 0.004 0.001 HIS B 249 PHE 0.016 0.002 PHE B 129 TYR 0.009 0.001 TYR A 436 ARG 0.002 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 0.521 Fit side-chains REVERT: A 65 MET cc_start: 0.8612 (tpp) cc_final: 0.8303 (ttm) outliers start: 24 outliers final: 16 residues processed: 107 average time/residue: 0.1273 time to fit residues: 18.7869 Evaluate side-chains 99 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 278 PHE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 373 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 37 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN A 129 ASN A 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4949 Z= 0.222 Angle : 0.633 9.018 6715 Z= 0.330 Chirality : 0.043 0.147 762 Planarity : 0.005 0.044 834 Dihedral : 5.034 26.075 665 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.61 % Allowed : 27.89 % Favored : 68.50 % 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: 0.07 (0.35), residues: 616 helix: 0.87 (0.29), residues: 365 sheet: -0.19 (0.55), residues: 101 loop : -1.66 (0.44), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 236 HIS 0.003 0.001 HIS B 249 PHE 0.023 0.002 PHE A 307 TYR 0.014 0.001 TYR A 287 ARG 0.001 0.000 ARG B 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.566 Fit side-chains REVERT: A 65 MET cc_start: 0.8550 (tpp) cc_final: 0.8284 (ttm) REVERT: A 438 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7703 (t80) outliers start: 19 outliers final: 17 residues processed: 100 average time/residue: 0.1335 time to fit residues: 18.4722 Evaluate side-chains 105 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 278 PHE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 438 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN A 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.167611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.122871 restraints weight = 7959.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.126441 restraints weight = 3836.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.128647 restraints weight = 2326.745| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4949 Z= 0.239 Angle : 0.643 9.432 6715 Z= 0.333 Chirality : 0.043 0.138 762 Planarity : 0.005 0.043 834 Dihedral : 5.015 25.410 665 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.80 % Allowed : 27.70 % Favored : 68.50 % 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: 0.08 (0.35), residues: 616 helix: 0.86 (0.29), residues: 368 sheet: -0.18 (0.55), residues: 101 loop : -1.69 (0.44), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 236 HIS 0.003 0.001 HIS B 249 PHE 0.015 0.001 PHE A 27 TYR 0.016 0.001 TYR A 287 ARG 0.001 0.000 ARG B 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1276.37 seconds wall clock time: 23 minutes 51.52 seconds (1431.52 seconds total)