Starting phenix.real_space_refine on Wed Mar 5 22:59:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7da5_30623/03_2025/7da5_30623.cif Found real_map, /net/cci-nas-00/data/ceres_data/7da5_30623/03_2025/7da5_30623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7da5_30623/03_2025/7da5_30623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7da5_30623/03_2025/7da5_30623.map" model { file = "/net/cci-nas-00/data/ceres_data/7da5_30623/03_2025/7da5_30623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7da5_30623/03_2025/7da5_30623.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.066 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 25 5.16 5 C 2611 2.51 5 N 683 2.21 5 O 694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4013 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2846 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 17, 'TRANS': 357} Chain breaks: 1 Chain: "B" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1167 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 205} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 534 Unresolved non-hydrogen angles: 684 Unresolved non-hydrogen dihedrals: 446 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 12, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 4, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 284 Time building chain proxies: 3.30, per 1000 atoms: 0.82 Number of scatterers: 4013 At special positions: 0 Unit cell: (102.883, 54.8145, 114.689, 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 25 16.00 O 694 8.00 N 683 7.00 C 2611 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.04 Conformation dependent library (CDL) restraints added in 721.7 milliseconds 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1056 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 4 sheets defined 62.6% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 17 through 34 removed outlier: 3.986A pdb=" N ALA A 21 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 52 Processing helix chain 'A' and resid 55 through 84 removed outlier: 5.568A pdb=" N ILE A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 85 through 104 Processing helix chain 'A' and resid 109 through 139 Proline residue: A 130 - end of helix removed outlier: 3.505A pdb=" N PHE A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 172 removed outlier: 4.441A pdb=" N SER A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Proline residue: A 155 - end of helix Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 173 through 192 removed outlier: 3.966A pdb=" N GLY A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N CYS A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 279 through 290 removed outlier: 6.062A pdb=" N SER A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 321 removed outlier: 4.294A pdb=" N VAL A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Proline residue: A 314 - end of helix removed outlier: 3.933A pdb=" N ASN A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 330 through 346 removed outlier: 4.102A pdb=" N SER A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 383 removed outlier: 3.995A pdb=" N TYR A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N MET A 379 " --> pdb=" O PHE A 375 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 415 removed outlier: 4.353A pdb=" N ILE A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 5.349A 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 removed outlier: 4.590A pdb=" N ARG A 411 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 449 removed outlier: 3.771A pdb=" N TYR A 423 " --> pdb=" O TYR A 419 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL A 428 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLY A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 153 through 156 Processing helix chain 'B' and resid 204 through 238 Proline residue: B 211 - end of helix removed outlier: 3.562A pdb=" N THR B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 4.542A pdb=" N VAL B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 33 Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63 removed outlier: 4.067A pdb=" N GLY B 95 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.501A pdb=" N ARG B 166 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 113 through 117 removed outlier: 6.449A pdb=" N GLU B 114 " --> pdb=" O ARG B 201 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ARG B 203 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILE B 116 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY B 192 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TRP B 139 " --> pdb=" O LEU B 150 " (cutoff:3.500A) 301 hydrogen bonds defined for protein. 873 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: 1.16 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 632 1.28 - 1.41: 1071 1.41 - 1.54: 2303 1.54 - 1.68: 58 1.68 - 1.81: 38 Bond restraints: 4102 Sorted by residual: bond pdb=" C PHE A 36 " pdb=" O PHE A 36 " ideal model delta sigma weight residual 1.238 1.144 0.094 1.28e-02 6.10e+03 5.39e+01 bond pdb=" CA ALA A 35 " pdb=" CB ALA A 35 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.02e-02 9.61e+03 2.92e+01 bond pdb=" N PRO B 91 " pdb=" CD PRO B 91 " ideal model delta sigma weight residual 1.474 1.539 -0.065 1.40e-02 5.10e+03 2.14e+01 bond pdb=" N PRO B 132 " pdb=" CD PRO B 132 " ideal model delta sigma weight residual 1.474 1.535 -0.061 1.40e-02 5.10e+03 1.93e+01 bond pdb=" CA VAL B 131 " pdb=" C VAL B 131 " ideal model delta sigma weight residual 1.524 1.557 -0.033 8.30e-03 1.45e+04 1.61e+01 ... (remaining 4097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 5394 2.89 - 5.78: 187 5.78 - 8.67: 13 8.67 - 11.56: 4 11.56 - 14.45: 4 Bond angle restraints: 5602 Sorted by residual: angle pdb=" CA PRO B 91 " pdb=" N PRO B 91 " pdb=" CD PRO B 91 " ideal model delta sigma weight residual 111.50 97.99 13.51 1.40e+00 5.10e-01 9.32e+01 angle pdb=" CA PRO B 132 " pdb=" N PRO B 132 " pdb=" CD PRO B 132 " ideal model delta sigma weight residual 111.50 98.10 13.40 1.40e+00 5.10e-01 9.16e+01 angle pdb=" CA PRO B 93 " pdb=" N PRO B 93 " pdb=" CD PRO B 93 " ideal model delta sigma weight residual 111.50 99.09 12.41 1.40e+00 5.10e-01 7.86e+01 angle pdb=" C TYR A 34 " pdb=" CA TYR A 34 " pdb=" CB TYR A 34 " ideal model delta sigma weight residual 111.45 125.90 -14.45 1.72e+00 3.38e-01 7.06e+01 angle pdb=" C PHE A 36 " pdb=" N PRO A 37 " pdb=" CA PRO A 37 " ideal model delta sigma weight residual 119.84 129.71 -9.87 1.25e+00 6.40e-01 6.24e+01 ... (remaining 5597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 2054 17.50 - 35.00: 208 35.00 - 52.50: 61 52.50 - 70.00: 11 70.00 - 87.50: 3 Dihedral angle restraints: 2337 sinusoidal: 675 harmonic: 1662 Sorted by residual: dihedral pdb=" C TYR A 34 " pdb=" N TYR A 34 " pdb=" CA TYR A 34 " pdb=" CB TYR A 34 " ideal model delta harmonic sigma weight residual -122.60 -142.16 19.56 0 2.50e+00 1.60e-01 6.12e+01 dihedral pdb=" C VAL B 50 " pdb=" N VAL B 50 " pdb=" CA VAL B 50 " pdb=" CB VAL B 50 " ideal model delta harmonic sigma weight residual -122.00 -139.09 17.09 0 2.50e+00 1.60e-01 4.67e+01 dihedral pdb=" N VAL B 50 " pdb=" C VAL B 50 " pdb=" CA VAL B 50 " pdb=" CB VAL B 50 " ideal model delta harmonic sigma weight residual 123.40 139.10 -15.70 0 2.50e+00 1.60e-01 3.94e+01 ... (remaining 2334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 610 0.130 - 0.259: 37 0.259 - 0.389: 7 0.389 - 0.518: 4 0.518 - 0.648: 3 Chirality restraints: 661 Sorted by residual: chirality pdb=" CA TYR A 34 " pdb=" N TYR A 34 " pdb=" C TYR A 34 " pdb=" CB TYR A 34 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA GLU B 172 " pdb=" N GLU B 172 " pdb=" C GLU B 172 " pdb=" CB GLU B 172 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.93e+00 chirality pdb=" CA VAL B 50 " pdb=" N VAL B 50 " pdb=" C VAL B 50 " pdb=" CB VAL B 50 " both_signs ideal model delta sigma weight residual False 2.44 1.88 0.56 2.00e-01 2.50e+01 7.77e+00 ... (remaining 658 not shown) Planarity restraints: 718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 36 " -0.063 2.00e-02 2.50e+03 5.57e-02 5.44e+01 pdb=" CG PHE A 36 " 0.129 2.00e-02 2.50e+03 pdb=" CD1 PHE A 36 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 36 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE A 36 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 36 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 36 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 36 " 0.032 2.00e-02 2.50e+03 6.63e-02 4.40e+01 pdb=" C PHE A 36 " -0.115 2.00e-02 2.50e+03 pdb=" O PHE A 36 " 0.044 2.00e-02 2.50e+03 pdb=" N PRO A 37 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 131 " 0.117 5.00e-02 4.00e+02 1.64e-01 4.29e+01 pdb=" N PRO B 132 " -0.282 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " 0.098 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " 0.067 5.00e-02 4.00e+02 ... (remaining 715 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 15 2.32 - 2.96: 2199 2.96 - 3.61: 5766 3.61 - 4.25: 8424 4.25 - 4.90: 14144 Nonbonded interactions: 30548 Sorted by model distance: nonbonded pdb=" O ILE A 171 " pdb=" NE ARG B 203 " model vdw 1.673 3.120 nonbonded pdb=" CB HIS B 115 " pdb=" NH2 ARG B 203 " model vdw 1.936 3.520 nonbonded pdb=" O GLY A 73 " pdb=" OG SER A 76 " model vdw 1.959 3.040 nonbonded pdb=" CG2 THR A 54 " pdb=" OE2 GLU A 57 " model vdw 2.028 3.460 nonbonded pdb=" O PRO A 74 " pdb=" OG SER A 77 " model vdw 2.058 3.040 ... (remaining 30543 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 14.990 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5515 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 : 0.008 0.094 4102 Z= 0.539 Angle : 1.210 14.454 5602 Z= 0.816 Chirality : 0.087 0.648 661 Planarity : 0.010 0.164 718 Dihedral : 16.471 87.496 1281 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.06 % Favored : 90.60 % Rotamer: Outliers : 10.06 % Allowed : 18.60 % Favored : 71.34 % Cbeta Deviations : 1.89 % Peptide Plane: Cis-proline : 11.11 % 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: -3.63 (0.31), residues: 585 helix: -2.39 (0.24), residues: 342 sheet: 0.31 (0.53), residues: 94 loop : -3.80 (0.40), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 18 HIS 0.001 0.000 HIS A 292 PHE 0.129 0.002 PHE A 36 TYR 0.047 0.002 TYR A 34 ARG 0.002 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 53 time to evaluate : 0.413 Fit side-chains REVERT: A 82 LYS cc_start: 0.7178 (tttt) cc_final: 0.6594 (mmtt) REVERT: B 115 HIS cc_start: 0.0400 (OUTLIER) cc_final: 0.0011 (p90) outliers start: 33 outliers final: 17 residues processed: 79 average time/residue: 0.1987 time to fit residues: 18.8879 Evaluate side-chains 57 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 226 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 127 ASN A 260 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.230463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.195350 restraints weight = 5824.164| |-----------------------------------------------------------------------------| r_work (start): 0.4392 rms_B_bonded: 2.46 r_work: 0.4305 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.4201 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4102 Z= 0.225 Angle : 0.699 6.943 5602 Z= 0.367 Chirality : 0.043 0.187 661 Planarity : 0.007 0.072 718 Dihedral : 6.724 49.010 646 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 5.79 % Allowed : 16.46 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.65 (0.34), residues: 585 helix: -0.62 (0.27), residues: 347 sheet: 0.84 (0.52), residues: 101 loop : -3.61 (0.45), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 60 HIS 0.002 0.001 HIS A 344 PHE 0.039 0.002 PHE A 332 TYR 0.020 0.002 TYR A 34 ARG 0.006 0.001 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.443 Fit side-chains REVERT: A 196 ARG cc_start: 0.7907 (tmt170) cc_final: 0.7512 (ttm170) outliers start: 19 outliers final: 10 residues processed: 72 average time/residue: 0.1590 time to fit residues: 15.2716 Evaluate side-chains 55 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 216 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 50 optimal weight: 0.0980 chunk 55 optimal weight: 0.0970 chunk 27 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 50.0000 chunk 7 optimal weight: 0.1980 chunk 43 optimal weight: 50.0000 chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.233045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.197262 restraints weight = 5701.717| |-----------------------------------------------------------------------------| r_work (start): 0.4412 rms_B_bonded: 2.43 r_work: 0.4321 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4220 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4102 Z= 0.187 Angle : 0.622 7.424 5602 Z= 0.323 Chirality : 0.040 0.153 661 Planarity : 0.005 0.071 718 Dihedral : 5.130 40.499 626 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.18 % Allowed : 18.90 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.71 (0.36), residues: 585 helix: 0.09 (0.29), residues: 349 sheet: 1.14 (0.53), residues: 101 loop : -3.12 (0.48), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 60 HIS 0.002 0.000 HIS A 344 PHE 0.019 0.001 PHE A 332 TYR 0.015 0.001 TYR A 113 ARG 0.003 0.001 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.383 Fit side-chains REVERT: A 135 ILE cc_start: 0.8715 (pp) cc_final: 0.8467 (mt) REVERT: A 151 MET cc_start: 0.7629 (tpp) cc_final: 0.7253 (mmm) REVERT: A 196 ARG cc_start: 0.7976 (tmt170) cc_final: 0.7512 (ttm170) outliers start: 17 outliers final: 10 residues processed: 61 average time/residue: 0.1259 time to fit residues: 10.2390 Evaluate side-chains 53 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 219 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 0.0020 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 50.0000 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 40.0000 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.218028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.182236 restraints weight = 5746.351| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 2.48 r_work: 0.4179 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.4077 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4102 Z= 0.283 Angle : 0.692 7.349 5602 Z= 0.368 Chirality : 0.044 0.150 661 Planarity : 0.006 0.074 718 Dihedral : 5.362 41.968 625 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 6.40 % Allowed : 19.82 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.35), residues: 585 helix: 0.03 (0.28), residues: 350 sheet: 1.48 (0.51), residues: 96 loop : -2.84 (0.49), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 174 HIS 0.006 0.002 HIS A 344 PHE 0.017 0.002 PHE A 356 TYR 0.019 0.003 TYR A 34 ARG 0.005 0.001 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.322 Fit side-chains REVERT: A 151 MET cc_start: 0.7721 (tpp) cc_final: 0.7356 (tpp) REVERT: A 188 CYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7766 (t) REVERT: A 414 ASP cc_start: 0.6834 (t0) cc_final: 0.6610 (t0) REVERT: A 415 MET cc_start: 0.6923 (ptm) cc_final: 0.6534 (ttt) outliers start: 21 outliers final: 8 residues processed: 80 average time/residue: 0.1168 time to fit residues: 12.5689 Evaluate side-chains 63 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 428 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 30.0000 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.218921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.182313 restraints weight = 5907.381| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 2.53 r_work: 0.4175 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4102 Z= 0.253 Angle : 0.685 8.446 5602 Z= 0.353 Chirality : 0.043 0.148 661 Planarity : 0.005 0.072 718 Dihedral : 5.244 41.447 625 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 6.71 % Allowed : 21.34 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.35), residues: 585 helix: 0.21 (0.28), residues: 351 sheet: 1.45 (0.52), residues: 96 loop : -2.66 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 174 HIS 0.004 0.001 HIS A 344 PHE 0.017 0.001 PHE A 169 TYR 0.015 0.002 TYR A 34 ARG 0.004 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.412 Fit side-chains REVERT: A 151 MET cc_start: 0.7388 (tpp) cc_final: 0.7170 (tpp) REVERT: A 414 ASP cc_start: 0.6565 (t0) cc_final: 0.6341 (t0) REVERT: A 415 MET cc_start: 0.6855 (ptm) cc_final: 0.6423 (ttt) outliers start: 22 outliers final: 13 residues processed: 75 average time/residue: 0.1170 time to fit residues: 11.9053 Evaluate side-chains 65 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain B residue 223 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 1 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 chunk 51 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 40.0000 chunk 57 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.214807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.178802 restraints weight = 5737.361| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 2.57 r_work: 0.4150 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4048 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4102 Z= 0.296 Angle : 0.709 8.210 5602 Z= 0.370 Chirality : 0.044 0.160 661 Planarity : 0.006 0.072 718 Dihedral : 5.410 41.594 625 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 6.10 % Allowed : 21.65 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.46 (0.35), residues: 585 helix: 0.18 (0.28), residues: 350 sheet: 1.24 (0.52), residues: 96 loop : -2.54 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 174 HIS 0.005 0.002 HIS A 344 PHE 0.023 0.002 PHE A 43 TYR 0.018 0.002 TYR A 34 ARG 0.002 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.449 Fit side-chains REVERT: A 151 MET cc_start: 0.7762 (tpp) cc_final: 0.7482 (tpp) REVERT: A 414 ASP cc_start: 0.6720 (t0) cc_final: 0.6490 (t0) REVERT: A 415 MET cc_start: 0.6992 (ptm) cc_final: 0.6547 (ttt) outliers start: 20 outliers final: 16 residues processed: 73 average time/residue: 0.1309 time to fit residues: 12.6754 Evaluate side-chains 70 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.212864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.177305 restraints weight = 5701.641| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 2.61 r_work: 0.4117 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4013 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4102 Z= 0.239 Angle : 0.681 7.514 5602 Z= 0.351 Chirality : 0.043 0.154 661 Planarity : 0.005 0.070 718 Dihedral : 5.288 41.655 625 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 7.62 % Allowed : 22.26 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.19 (0.35), residues: 585 helix: 0.47 (0.28), residues: 347 sheet: 1.20 (0.53), residues: 96 loop : -2.48 (0.49), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 174 HIS 0.005 0.001 HIS A 344 PHE 0.024 0.002 PHE A 43 TYR 0.015 0.002 TYR A 34 ARG 0.004 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 56 time to evaluate : 0.405 Fit side-chains REVERT: A 151 MET cc_start: 0.7671 (tpp) cc_final: 0.7332 (tpp) REVERT: A 415 MET cc_start: 0.6881 (ptm) cc_final: 0.6544 (ttt) REVERT: B 203 ARG cc_start: 0.3324 (mtt90) cc_final: 0.3045 (mtt90) outliers start: 25 outliers final: 16 residues processed: 75 average time/residue: 0.1062 time to fit residues: 10.9668 Evaluate side-chains 73 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain B residue 216 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.209639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.174394 restraints weight = 5637.682| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 2.59 r_work: 0.4112 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4007 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 4102 Z= 0.302 Angle : 0.730 11.528 5602 Z= 0.379 Chirality : 0.045 0.156 661 Planarity : 0.006 0.073 718 Dihedral : 5.461 42.995 625 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 6.71 % Allowed : 21.95 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.44 (0.35), residues: 585 helix: 0.21 (0.28), residues: 349 sheet: 0.95 (0.55), residues: 96 loop : -2.30 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 18 HIS 0.006 0.001 HIS A 344 PHE 0.024 0.002 PHE A 43 TYR 0.018 0.002 TYR A 34 ARG 0.004 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.382 Fit side-chains REVERT: A 140 TYR cc_start: 0.4769 (m-10) cc_final: 0.4161 (t80) REVERT: A 151 MET cc_start: 0.7630 (tpp) cc_final: 0.7389 (tpp) REVERT: B 203 ARG cc_start: 0.3442 (mtt90) cc_final: 0.3134 (mtt90) outliers start: 22 outliers final: 16 residues processed: 76 average time/residue: 0.1064 time to fit residues: 11.2113 Evaluate side-chains 70 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.210654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.175624 restraints weight = 5675.642| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 2.62 r_work: 0.4112 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.4006 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.5956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4102 Z= 0.275 Angle : 0.712 10.035 5602 Z= 0.362 Chirality : 0.043 0.153 661 Planarity : 0.005 0.072 718 Dihedral : 5.350 41.378 625 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.18 % Allowed : 25.00 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.25 (0.35), residues: 585 helix: 0.44 (0.28), residues: 346 sheet: 1.27 (0.56), residues: 88 loop : -2.41 (0.48), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 60 HIS 0.005 0.001 HIS A 344 PHE 0.017 0.002 PHE A 332 TYR 0.018 0.002 TYR A 34 ARG 0.003 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.432 Fit side-chains REVERT: A 151 MET cc_start: 0.7542 (tpp) cc_final: 0.7263 (tpp) REVERT: B 203 ARG cc_start: 0.3196 (mtt90) cc_final: 0.2884 (mtt90) outliers start: 17 outliers final: 15 residues processed: 71 average time/residue: 0.1126 time to fit residues: 11.0861 Evaluate side-chains 69 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 30.0000 chunk 33 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.211701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.176697 restraints weight = 5661.355| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 2.61 r_work: 0.4120 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4014 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.6280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4102 Z= 0.231 Angle : 0.710 10.409 5602 Z= 0.358 Chirality : 0.042 0.147 661 Planarity : 0.005 0.069 718 Dihedral : 5.231 41.275 625 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 5.79 % Allowed : 25.00 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.36), residues: 585 helix: 0.48 (0.29), residues: 350 sheet: 1.27 (0.58), residues: 87 loop : -2.43 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 60 HIS 0.004 0.001 HIS A 344 PHE 0.016 0.001 PHE A 332 TYR 0.020 0.002 TYR A 140 ARG 0.002 0.000 ARG A 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.406 Fit side-chains REVERT: A 151 MET cc_start: 0.7491 (tpp) cc_final: 0.7216 (tpp) REVERT: A 415 MET cc_start: 0.6716 (ptm) cc_final: 0.6382 (tpt) REVERT: B 203 ARG cc_start: 0.3252 (mtt90) cc_final: 0.2879 (mtt90) outliers start: 19 outliers final: 16 residues processed: 73 average time/residue: 0.1119 time to fit residues: 11.2425 Evaluate side-chains 68 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 30.0000 chunk 52 optimal weight: 4.9990 chunk 10 optimal weight: 0.0170 chunk 31 optimal weight: 0.9990 chunk 39 optimal weight: 50.0000 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.210827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.176052 restraints weight = 5706.444| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 2.67 r_work: 0.4109 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.6445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4102 Z= 0.245 Angle : 0.729 13.077 5602 Z= 0.363 Chirality : 0.043 0.148 661 Planarity : 0.005 0.069 718 Dihedral : 5.213 40.620 625 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.88 % Allowed : 26.83 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.25 (0.36), residues: 585 helix: 0.49 (0.28), residues: 350 sheet: 1.21 (0.58), residues: 87 loop : -2.56 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 60 HIS 0.004 0.001 HIS A 344 PHE 0.017 0.001 PHE A 332 TYR 0.018 0.002 TYR A 140 ARG 0.002 0.000 ARG A 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2534.44 seconds wall clock time: 43 minutes 58.93 seconds (2638.93 seconds total)