Starting phenix.real_space_refine on Fri Aug 22 14:18:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7da5_30623/08_2025/7da5_30623.cif Found real_map, /net/cci-nas-00/data/ceres_data/7da5_30623/08_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_30623/08_2025/7da5_30623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7da5_30623/08_2025/7da5_30623.map" model { file = "/net/cci-nas-00/data/ceres_data/7da5_30623/08_2025/7da5_30623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7da5_30623/08_2025/7da5_30623.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'PHE:plan': 5, 'GLU:plan': 16, 'ASP:plan': 12, 'ASN:plan1': 7, 'HIS:plan': 3, 'ARG:plan': 6, 'TRP:plan': 4, 'GLN:plan1': 6, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 284 Time building chain proxies: 1.20, per 1000 atoms: 0.30 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: 0.34 Conformation dependent library (CDL) restraints added in 122.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.08 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: 0.48 Time building geometry restraints manager: 0.43 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: 1.190 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.970 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.400 ------------------------------------------------------------------------------- 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= 0.552 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 196 TYR 0.047 0.002 TYR A 34 PHE 0.129 0.002 PHE A 36 TRP 0.005 0.001 TRP A 18 HIS 0.001 0.000 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00803 ( 4102) covalent geometry : angle 1.20979 ( 5602) hydrogen bonds : bond 0.14736 ( 301) hydrogen bonds : angle 7.41181 ( 873) *********************** 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 : 0.118 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: 0.0109 (p90) outliers start: 33 outliers final: 17 residues processed: 79 average time/residue: 0.0770 time to fit residues: 7.2692 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 : 0.096 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 50 optimal weight: 5.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.4762 r_free = 0.4762 target = 0.232201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.196360 restraints weight = 5874.887| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 2.48 r_work: 0.4309 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4102 Z= 0.160 Angle : 0.692 6.872 5602 Z= 0.363 Chirality : 0.042 0.192 661 Planarity : 0.007 0.072 718 Dihedral : 6.694 49.019 646 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 5.49 % Allowed : 16.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.34), residues: 585 helix: -0.60 (0.28), residues: 349 sheet: 0.83 (0.52), residues: 101 loop : -3.59 (0.45), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 446 TYR 0.022 0.002 TYR A 34 PHE 0.036 0.002 PHE A 332 TRP 0.016 0.001 TRP A 60 HIS 0.002 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 4102) covalent geometry : angle 0.69202 ( 5602) hydrogen bonds : bond 0.05020 ( 301) hydrogen bonds : angle 5.25775 ( 873) *********************** 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 72 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.138 Fit side-chains REVERT: A 196 ARG cc_start: 0.7816 (tmt170) cc_final: 0.7416 (ttm170) outliers start: 18 outliers final: 9 residues processed: 69 average time/residue: 0.0456 time to fit residues: 4.4249 Evaluate side-chains 51 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL 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 52 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 chunk 38 optimal weight: 50.0000 chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4757 r_free = 0.4757 target = 0.231847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.195520 restraints weight = 5830.581| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 2.50 r_work: 0.4298 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4102 Z= 0.143 Angle : 0.629 7.503 5602 Z= 0.329 Chirality : 0.041 0.157 661 Planarity : 0.006 0.071 718 Dihedral : 5.179 40.645 626 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 6.10 % Allowed : 17.68 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.36), residues: 585 helix: -0.03 (0.29), residues: 350 sheet: 1.16 (0.52), residues: 101 loop : -3.10 (0.49), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 203 TYR 0.016 0.001 TYR A 113 PHE 0.019 0.001 PHE A 332 TRP 0.012 0.001 TRP A 174 HIS 0.002 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 4102) covalent geometry : angle 0.62909 ( 5602) hydrogen bonds : bond 0.04725 ( 301) hydrogen bonds : angle 4.88503 ( 873) *********************** 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 71 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 0.083 Fit side-chains REVERT: A 151 MET cc_start: 0.7269 (tpp) cc_final: 0.7015 (mmm) REVERT: A 196 ARG cc_start: 0.7902 (tmt170) cc_final: 0.7536 (ttm170) outliers start: 20 outliers final: 11 residues processed: 66 average time/residue: 0.0402 time to fit residues: 3.5057 Evaluate side-chains 57 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 MET 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 275 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 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 57 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4654 r_free = 0.4654 target = 0.219440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.183602 restraints weight = 5760.402| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 2.53 r_work: 0.4201 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4097 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4102 Z= 0.171 Angle : 0.646 7.477 5602 Z= 0.343 Chirality : 0.043 0.149 661 Planarity : 0.006 0.073 718 Dihedral : 5.193 40.644 625 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 7.32 % Allowed : 18.60 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.35), residues: 585 helix: 0.16 (0.28), residues: 351 sheet: 1.53 (0.51), residues: 96 loop : -2.77 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 201 TYR 0.018 0.002 TYR A 34 PHE 0.020 0.002 PHE A 387 TRP 0.007 0.001 TRP A 174 HIS 0.005 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 4102) covalent geometry : angle 0.64630 ( 5602) hydrogen bonds : bond 0.05057 ( 301) hydrogen bonds : angle 4.83788 ( 873) *********************** 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 86 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.122 Fit side-chains REVERT: A 140 TYR cc_start: 0.4785 (m-10) cc_final: 0.4179 (t80) REVERT: A 151 MET cc_start: 0.7665 (tpp) cc_final: 0.7292 (mmm) REVERT: A 415 MET cc_start: 0.6791 (ptm) cc_final: 0.6393 (tpt) outliers start: 24 outliers final: 11 residues processed: 79 average time/residue: 0.0430 time to fit residues: 4.6292 Evaluate side-chains 69 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 275 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 408 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 115 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.0770 chunk 12 optimal weight: 0.0070 chunk 8 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 40 optimal weight: 40.0000 chunk 48 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 HIS A 413 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.226638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.189783 restraints weight = 5685.220| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 2.47 r_work: 0.4264 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.4161 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4102 Z= 0.134 Angle : 0.646 7.753 5602 Z= 0.325 Chirality : 0.041 0.130 661 Planarity : 0.005 0.068 718 Dihedral : 4.972 40.770 625 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 6.10 % Allowed : 21.34 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.36), residues: 585 helix: 0.55 (0.29), residues: 351 sheet: 1.58 (0.51), residues: 96 loop : -2.54 (0.50), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 201 TYR 0.014 0.001 TYR A 113 PHE 0.018 0.001 PHE A 169 TRP 0.012 0.001 TRP A 60 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 4102) covalent geometry : angle 0.64572 ( 5602) hydrogen bonds : bond 0.04344 ( 301) hydrogen bonds : angle 4.51934 ( 873) *********************** 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 72 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.084 Fit side-chains REVERT: A 140 TYR cc_start: 0.4775 (m-10) cc_final: 0.4148 (t80) REVERT: A 151 MET cc_start: 0.7659 (tpp) cc_final: 0.7209 (mmm) REVERT: A 196 ARG cc_start: 0.7802 (tmt170) cc_final: 0.7518 (ttt180) REVERT: B 203 ARG cc_start: 0.2422 (mtt90) cc_final: 0.2180 (mtt90) outliers start: 20 outliers final: 13 residues processed: 68 average time/residue: 0.0546 time to fit residues: 4.6582 Evaluate side-chains 59 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 275 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 381 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain B residue 115 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 0.0010 chunk 26 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 39 optimal weight: 40.0000 chunk 49 optimal weight: 8.9990 chunk 38 optimal weight: 50.0000 chunk 5 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.1190 ------------------------------------------------------------------------------- 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 = 0.4665 r_free = 0.4665 target = 0.221202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.184290 restraints weight = 5856.868| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 2.54 r_work: 0.4202 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.4098 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4102 Z= 0.160 Angle : 0.663 8.753 5602 Z= 0.339 Chirality : 0.042 0.138 661 Planarity : 0.005 0.068 718 Dihedral : 5.141 42.572 625 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 6.40 % Allowed : 21.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.36), residues: 585 helix: 0.54 (0.29), residues: 351 sheet: 1.63 (0.51), residues: 96 loop : -2.56 (0.50), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 446 TYR 0.017 0.002 TYR A 113 PHE 0.012 0.001 PHE A 169 TRP 0.014 0.001 TRP A 174 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 4102) covalent geometry : angle 0.66319 ( 5602) hydrogen bonds : bond 0.04656 ( 301) hydrogen bonds : angle 4.62903 ( 873) *********************** 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 77 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.109 Fit side-chains REVERT: A 151 MET cc_start: 0.7716 (tpp) cc_final: 0.7296 (mmm) outliers start: 21 outliers final: 11 residues processed: 73 average time/residue: 0.0431 time to fit residues: 4.2419 Evaluate side-chains 62 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 138 TYR 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 428 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 30.0000 chunk 2 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 30.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 291 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.215369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.178599 restraints weight = 5819.000| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 2.65 r_work: 0.4143 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.5245 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= 0.173 Angle : 0.678 9.336 5602 Z= 0.350 Chirality : 0.043 0.157 661 Planarity : 0.005 0.071 718 Dihedral : 5.195 41.642 625 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 6.10 % Allowed : 21.34 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.35), residues: 585 helix: 0.53 (0.28), residues: 347 sheet: 1.61 (0.52), residues: 96 loop : -2.50 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 446 TYR 0.017 0.002 TYR A 34 PHE 0.015 0.002 PHE A 332 TRP 0.018 0.001 TRP A 174 HIS 0.006 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 4102) covalent geometry : angle 0.67844 ( 5602) hydrogen bonds : bond 0.04830 ( 301) hydrogen bonds : angle 4.71192 ( 873) *********************** 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 74 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.138 Fit side-chains REVERT: A 151 MET cc_start: 0.7268 (tpp) cc_final: 0.7033 (tpp) outliers start: 20 outliers final: 14 residues processed: 69 average time/residue: 0.0402 time to fit residues: 3.8839 Evaluate side-chains 65 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 281 LEU 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 394 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 219 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 26 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.4585 r_free = 0.4585 target = 0.212482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.175999 restraints weight = 5734.208| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 2.64 r_work: 0.4107 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.4005 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4102 Z= 0.197 Angle : 0.720 10.341 5602 Z= 0.372 Chirality : 0.044 0.177 661 Planarity : 0.006 0.074 718 Dihedral : 5.376 42.047 625 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 6.10 % Allowed : 22.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.35), residues: 585 helix: 0.37 (0.28), residues: 347 sheet: 1.44 (0.53), residues: 96 loop : -2.32 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 446 TYR 0.021 0.002 TYR A 34 PHE 0.012 0.002 PHE A 263 TRP 0.022 0.002 TRP A 174 HIS 0.005 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 4102) covalent geometry : angle 0.72036 ( 5602) hydrogen bonds : bond 0.05068 ( 301) hydrogen bonds : angle 4.84763 ( 873) *********************** 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 75 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.128 Fit side-chains REVERT: B 203 ARG cc_start: 0.3028 (mtt90) cc_final: 0.2582 (mtt90) outliers start: 20 outliers final: 15 residues processed: 71 average time/residue: 0.0417 time to fit residues: 4.1585 Evaluate side-chains 67 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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 281 LEU 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 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 115 HIS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 219 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 44 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 53 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4611 r_free = 0.4611 target = 0.216139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.180071 restraints weight = 5821.700| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 2.64 r_work: 0.4145 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.5758 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= 0.145 Angle : 0.679 10.129 5602 Z= 0.340 Chirality : 0.044 0.314 661 Planarity : 0.005 0.070 718 Dihedral : 5.111 40.276 625 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.57 % Allowed : 25.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.36), residues: 585 helix: 0.70 (0.29), residues: 345 sheet: 1.48 (0.53), residues: 96 loop : -2.35 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 446 TYR 0.016 0.002 TYR A 34 PHE 0.010 0.001 PHE A 169 TRP 0.015 0.001 TRP A 174 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4102) covalent geometry : angle 0.67883 ( 5602) hydrogen bonds : bond 0.04490 ( 301) hydrogen bonds : angle 4.58676 ( 873) *********************** 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 68 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.113 Fit side-chains outliers start: 15 outliers final: 14 residues processed: 65 average time/residue: 0.0463 time to fit residues: 3.9435 Evaluate side-chains 64 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.082 ------------------------------------------------------------------------------- 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 198 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 349 LEU 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 115 HIS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 219 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 30.0000 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 30.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4613 r_free = 0.4613 target = 0.216152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.180574 restraints weight = 5678.771| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 2.60 r_work: 0.4148 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4044 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.5934 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= 0.147 Angle : 0.709 13.588 5602 Z= 0.348 Chirality : 0.044 0.311 661 Planarity : 0.005 0.069 718 Dihedral : 5.117 42.009 625 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.27 % Allowed : 25.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.36), residues: 585 helix: 0.66 (0.29), residues: 348 sheet: 1.52 (0.54), residues: 95 loop : -2.30 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 446 TYR 0.019 0.002 TYR A 34 PHE 0.024 0.001 PHE A 169 TRP 0.016 0.001 TRP A 174 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 4102) covalent geometry : angle 0.70886 ( 5602) hydrogen bonds : bond 0.04419 ( 301) hydrogen bonds : angle 4.50590 ( 873) ********************** 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 66 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.136 Fit side-chains REVERT: A 138 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.6926 (t80) REVERT: A 151 MET cc_start: 0.7577 (tpp) cc_final: 0.7248 (mmm) REVERT: B 203 ARG cc_start: 0.3005 (mtt90) cc_final: 0.2787 (mtt90) outliers start: 14 outliers final: 11 residues processed: 62 average time/residue: 0.0512 time to fit residues: 4.2600 Evaluate side-chains 61 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 349 LEU 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 115 HIS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 219 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 50.0000 chunk 57 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 45 optimal weight: 30.0000 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 46 optimal weight: 0.0970 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4635 r_free = 0.4635 target = 0.218298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.182263 restraints weight = 5744.141| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 2.68 r_work: 0.4176 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.6077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4102 Z= 0.137 Angle : 0.681 13.115 5602 Z= 0.335 Chirality : 0.042 0.245 661 Planarity : 0.005 0.068 718 Dihedral : 4.967 39.869 625 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.27 % Allowed : 25.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.36), residues: 585 helix: 0.83 (0.29), residues: 346 sheet: 1.48 (0.54), residues: 95 loop : -2.29 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 446 TYR 0.018 0.001 TYR A 34 PHE 0.023 0.001 PHE A 169 TRP 0.014 0.001 TRP A 174 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 4102) covalent geometry : angle 0.68120 ( 5602) hydrogen bonds : bond 0.04207 ( 301) hydrogen bonds : angle 4.42327 ( 873) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1087.42 seconds wall clock time: 19 minutes 15.46 seconds (1155.46 seconds total)