Starting phenix.real_space_refine on Wed Sep 17 09:30:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dka_46949/09_2025/9dka_46949_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dka_46949/09_2025/9dka_46949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dka_46949/09_2025/9dka_46949_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dka_46949/09_2025/9dka_46949_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dka_46949/09_2025/9dka_46949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dka_46949/09_2025/9dka_46949.map" } resolution = 3.0 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= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Br 2 7.06 5 S 26 5.16 5 C 2501 2.51 5 N 656 2.21 5 O 662 1.98 5 H 3879 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7726 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 7704 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 30, 'TRANS': 486} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'R75': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.74, per 1000 atoms: 0.23 Number of scatterers: 7726 At special positions: 0 Unit cell: (79.515, 90.63, 84.645, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 2 34.99 S 26 16.00 O 662 8.00 N 656 7.00 C 2501 6.00 H 3879 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 139 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 468.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 3 sheets defined 80.9% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.924A pdb=" N LEU A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 37 Proline residue: A 27 - end of helix removed outlier: 4.185A pdb=" N TRP A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.757A pdb=" N VAL A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 74 removed outlier: 3.820A pdb=" N ALA A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 130 through 136 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 143 through 171 removed outlier: 3.588A pdb=" N ILE A 156 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Proline residue: A 165 - end of helix removed outlier: 3.578A pdb=" N ARG A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 192 removed outlier: 3.652A pdb=" N PHE A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 224 removed outlier: 3.621A pdb=" N TRP A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 253 removed outlier: 3.821A pdb=" N THR A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 267 through 276 removed outlier: 4.138A pdb=" N LEU A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 291 through 307 Processing helix chain 'A' and resid 308 through 315 removed outlier: 3.641A pdb=" N LEU A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 324 Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.911A pdb=" N VAL A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 removed outlier: 3.810A pdb=" N THR A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 368 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 377 through 403 removed outlier: 3.974A pdb=" N LEU A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) Proline residue: A 391 - end of helix removed outlier: 3.758A pdb=" N LEU A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 424 removed outlier: 3.646A pdb=" N THR A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 460 removed outlier: 3.534A pdb=" N THR A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLY A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 459 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 486 Proline residue: A 484 - end of helix Processing helix chain 'A' and resid 487 through 493 removed outlier: 3.593A pdb=" N VAL A 491 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 513 removed outlier: 4.087A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Proline residue: A 505 - end of helix removed outlier: 3.647A pdb=" N LEU A 513 " --> pdb=" O GLY A 509 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80 removed outlier: 3.950A pdb=" N GLY A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 264 hydrogen bonds defined for protein. 771 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: 1.82 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.06: 3870 1.06 - 1.28: 604 1.28 - 1.50: 1691 1.50 - 1.72: 1611 1.72 - 1.94: 41 Bond restraints: 7817 Sorted by residual: bond pdb=" CAC R75 A 601 " pdb=" OAG R75 A 601 " ideal model delta sigma weight residual 1.326 1.397 -0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" CAJ R75 A 601 " pdb=" CAL R75 A 601 " ideal model delta sigma weight residual 1.465 1.531 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" CAB R75 A 601 " pdb="BR2 R75 A 601 " ideal model delta sigma weight residual 1.880 1.944 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" CAD R75 A 601 " pdb="BR1 R75 A 601 " ideal model delta sigma weight residual 1.884 1.944 -0.060 2.00e-02 2.50e+03 9.05e+00 bond pdb=" CAF R75 A 601 " pdb=" CAJ R75 A 601 " ideal model delta sigma weight residual 1.485 1.533 -0.048 2.00e-02 2.50e+03 5.67e+00 ... (remaining 7812 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.02: 14150 6.02 - 12.04: 4 12.04 - 18.06: 0 18.06 - 24.07: 2 24.07 - 30.09: 4 Bond angle restraints: 14160 Sorted by residual: angle pdb=" CA ALA A 103 " pdb=" CB ALA A 103 " pdb=" HB3 ALA A 103 " ideal model delta sigma weight residual 109.00 78.91 30.09 3.00e+00 1.11e-01 1.01e+02 angle pdb=" HB2 ALA A 103 " pdb=" CB ALA A 103 " pdb=" HB3 ALA A 103 " ideal model delta sigma weight residual 110.00 80.70 29.30 3.00e+00 1.11e-01 9.54e+01 angle pdb=" CA ALA A 103 " pdb=" CB ALA A 103 " pdb=" HB1 ALA A 103 " ideal model delta sigma weight residual 109.00 80.22 28.78 3.00e+00 1.11e-01 9.20e+01 angle pdb=" HB1 ALA A 103 " pdb=" CB ALA A 103 " pdb=" HB2 ALA A 103 " ideal model delta sigma weight residual 110.00 81.39 28.61 3.00e+00 1.11e-01 9.10e+01 angle pdb=" HB1 ALA A 103 " pdb=" CB ALA A 103 " pdb=" HB3 ALA A 103 " ideal model delta sigma weight residual 110.00 132.26 -22.26 3.00e+00 1.11e-01 5.51e+01 ... (remaining 14155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.89: 3491 34.89 - 69.78: 179 69.78 - 104.67: 12 104.67 - 139.56: 0 139.56 - 174.45: 1 Dihedral angle restraints: 3683 sinusoidal: 1980 harmonic: 1703 Sorted by residual: dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 116 " pdb=" CB CYS A 116 " ideal model delta sinusoidal sigma weight residual -86.00 -160.16 74.16 1 1.00e+01 1.00e-02 6.98e+01 dihedral pdb=" CAL R75 A 601 " pdb=" CAM R75 A 601 " pdb=" CAQ R75 A 601 " pdb=" CAR R75 A 601 " ideal model delta sinusoidal sigma weight residual -96.04 78.41 -174.45 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA LEU A 99 " pdb=" C LEU A 99 " pdb=" N ASP A 100 " pdb=" CA ASP A 100 " ideal model delta harmonic sigma weight residual -180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 3680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 396 0.024 - 0.048: 142 0.048 - 0.072: 61 0.072 - 0.096: 31 0.096 - 0.120: 12 Chirality restraints: 642 Sorted by residual: chirality pdb=" CA VAL A 121 " pdb=" N VAL A 121 " pdb=" C VAL A 121 " pdb=" CB VAL A 121 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.61e-01 chirality pdb=" CA VAL A 63 " pdb=" N VAL A 63 " pdb=" C VAL A 63 " pdb=" CB VAL A 63 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.61e-01 chirality pdb=" CA ASP A 100 " pdb=" N ASP A 100 " pdb=" C ASP A 100 " pdb=" CB ASP A 100 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.60e-01 ... (remaining 639 not shown) Planarity restraints: 1164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 434 " -0.285 9.50e-02 1.11e+02 9.51e-02 9.81e+00 pdb=" NE ARG A 434 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 434 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 434 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 434 " -0.003 2.00e-02 2.50e+03 pdb="HH11 ARG A 434 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 434 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 434 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG A 434 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 100 " 0.049 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO A 101 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 26 " 0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO A 27 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " 0.029 5.00e-02 4.00e+02 ... (remaining 1161 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.22: 604 2.22 - 2.84: 17000 2.84 - 3.46: 21013 3.46 - 4.08: 28708 4.08 - 4.70: 45605 Nonbonded interactions: 112930 Sorted by model distance: nonbonded pdb=" O GLN A 17 " pdb=" HG1 THR A 21 " model vdw 1.595 2.450 nonbonded pdb="HE21 GLN A 17 " pdb=" O TRP A 224 " model vdw 1.656 2.450 nonbonded pdb=" O SER A 336 " pdb=" HG1 THR A 339 " model vdw 1.674 2.450 nonbonded pdb=" OE1 GLU A 70 " pdb=" H GLU A 70 " model vdw 1.691 2.450 nonbonded pdb=" HH TYR A 122 " pdb=" OD1 ASP A 136 " model vdw 1.703 2.450 ... (remaining 112925 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.210 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: 0.050 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.090 Find NCS groups from input model: 0.020 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:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 3940 Z= 0.177 Angle : 0.611 8.567 5391 Z= 0.297 Chirality : 0.036 0.120 642 Planarity : 0.007 0.125 678 Dihedral : 17.105 174.451 1355 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.55 % Favored : 98.25 % Rotamer: Outliers : 0.52 % Allowed : 29.12 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.64 (0.38), residues: 515 helix: 1.07 (0.28), residues: 370 sheet: -4.96 (1.17), residues: 10 loop : -0.79 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 48 TYR 0.010 0.001 TYR A 275 PHE 0.013 0.001 PHE A 241 TRP 0.008 0.001 TRP A 96 HIS 0.003 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 3938) covalent geometry : angle 0.61108 ( 5387) SS BOND : bond 0.00093 ( 2) SS BOND : angle 0.37864 ( 4) hydrogen bonds : bond 0.18557 ( 264) hydrogen bonds : angle 6.91645 ( 771) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 102 average time/residue: 0.7508 time to fit residues: 80.5619 Evaluate side-chains 59 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.088170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.068128 restraints weight = 23809.545| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.66 r_work: 0.2855 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3940 Z= 0.183 Angle : 0.655 6.739 5391 Z= 0.341 Chirality : 0.037 0.124 642 Planarity : 0.005 0.040 678 Dihedral : 8.946 157.769 555 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.09 % Allowed : 31.70 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.37), residues: 515 helix: 1.61 (0.27), residues: 374 sheet: -4.48 (1.19), residues: 10 loop : -0.91 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 230 TYR 0.016 0.002 TYR A 275 PHE 0.017 0.001 PHE A 362 TRP 0.004 0.001 TRP A 30 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 3938) covalent geometry : angle 0.65527 ( 5387) SS BOND : bond 0.00074 ( 2) SS BOND : angle 0.37454 ( 4) hydrogen bonds : bond 0.06267 ( 264) hydrogen bonds : angle 4.65329 ( 771) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 74 average time/residue: 0.6917 time to fit residues: 54.1050 Evaluate side-chains 68 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 518 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 42 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3357 r_free = 0.3357 target = 0.088876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.068909 restraints weight = 23611.000| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.62 r_work: 0.2869 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 3940 Z= 0.149 Angle : 0.613 5.494 5391 Z= 0.316 Chirality : 0.037 0.148 642 Planarity : 0.005 0.039 678 Dihedral : 8.700 149.906 555 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.61 % Allowed : 30.41 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.81 (0.39), residues: 515 helix: 1.93 (0.27), residues: 364 sheet: -3.94 (1.47), residues: 10 loop : -0.26 (0.58), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 230 TYR 0.016 0.001 TYR A 275 PHE 0.012 0.001 PHE A 360 TRP 0.004 0.001 TRP A 30 HIS 0.001 0.000 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 3938) covalent geometry : angle 0.61344 ( 5387) SS BOND : bond 0.00097 ( 2) SS BOND : angle 0.30132 ( 4) hydrogen bonds : bond 0.05477 ( 264) hydrogen bonds : angle 4.36842 ( 771) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 VAL cc_start: 0.8412 (OUTLIER) cc_final: 0.8179 (t) REVERT: A 326 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8592 (tm-30) REVERT: A 370 ASP cc_start: 0.6863 (OUTLIER) cc_final: 0.6454 (p0) outliers start: 14 outliers final: 6 residues processed: 77 average time/residue: 0.7560 time to fit residues: 61.4314 Evaluate side-chains 61 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 518 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3345 r_free = 0.3345 target = 0.088126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.068157 restraints weight = 23683.738| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.63 r_work: 0.2850 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3940 Z= 0.161 Angle : 0.598 5.244 5391 Z= 0.311 Chirality : 0.037 0.151 642 Planarity : 0.005 0.035 678 Dihedral : 8.548 144.910 555 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.35 % Allowed : 28.35 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.58 (0.38), residues: 515 helix: 1.91 (0.27), residues: 371 sheet: -3.80 (1.52), residues: 10 loop : -1.02 (0.52), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 230 TYR 0.016 0.001 TYR A 275 PHE 0.012 0.001 PHE A 362 TRP 0.006 0.001 TRP A 30 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 3938) covalent geometry : angle 0.59844 ( 5387) SS BOND : bond 0.00078 ( 2) SS BOND : angle 0.17760 ( 4) hydrogen bonds : bond 0.05182 ( 264) hydrogen bonds : angle 4.25124 ( 771) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8565 (tm-30) outliers start: 13 outliers final: 8 residues processed: 70 average time/residue: 0.7262 time to fit residues: 53.7293 Evaluate side-chains 65 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 518 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 32 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.087443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.067869 restraints weight = 23203.744| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.56 r_work: 0.2839 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3940 Z= 0.173 Angle : 0.588 4.848 5391 Z= 0.307 Chirality : 0.036 0.125 642 Planarity : 0.005 0.042 678 Dihedral : 8.472 141.617 555 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.58 % Allowed : 31.70 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.96 (0.39), residues: 515 helix: 2.10 (0.28), residues: 362 sheet: -3.66 (1.53), residues: 10 loop : -0.36 (0.56), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 230 TYR 0.016 0.002 TYR A 275 PHE 0.013 0.001 PHE A 362 TRP 0.006 0.001 TRP A 285 HIS 0.002 0.000 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 3938) covalent geometry : angle 0.58779 ( 5387) SS BOND : bond 0.00106 ( 2) SS BOND : angle 0.14113 ( 4) hydrogen bonds : bond 0.05063 ( 264) hydrogen bonds : angle 4.22996 ( 771) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.7864 (tp30) cc_final: 0.7372 (pm20) outliers start: 10 outliers final: 9 residues processed: 64 average time/residue: 0.7935 time to fit residues: 53.4681 Evaluate side-chains 61 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 32 CYS Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 518 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3349 r_free = 0.3349 target = 0.088187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.068716 restraints weight = 23115.546| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.57 r_work: 0.2853 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3940 Z= 0.141 Angle : 0.578 4.768 5391 Z= 0.298 Chirality : 0.035 0.122 642 Planarity : 0.005 0.048 678 Dihedral : 8.305 138.722 555 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.09 % Allowed : 30.41 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.81 (0.39), residues: 515 helix: 2.08 (0.28), residues: 371 sheet: -3.50 (1.59), residues: 10 loop : -0.96 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 230 TYR 0.015 0.001 TYR A 275 PHE 0.011 0.001 PHE A 208 TRP 0.006 0.001 TRP A 285 HIS 0.002 0.000 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 3938) covalent geometry : angle 0.57834 ( 5387) SS BOND : bond 0.00086 ( 2) SS BOND : angle 0.21681 ( 4) hydrogen bonds : bond 0.04743 ( 264) hydrogen bonds : angle 4.07672 ( 771) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.7892 (tp30) cc_final: 0.7446 (pm20) REVERT: A 370 ASP cc_start: 0.7007 (OUTLIER) cc_final: 0.6610 (p0) outliers start: 12 outliers final: 9 residues processed: 67 average time/residue: 0.7642 time to fit residues: 54.0065 Evaluate side-chains 67 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 518 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.088860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.069388 restraints weight = 22889.523| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.56 r_work: 0.2880 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3940 Z= 0.121 Angle : 0.579 6.364 5391 Z= 0.293 Chirality : 0.035 0.123 642 Planarity : 0.005 0.057 678 Dihedral : 8.135 135.708 555 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.84 % Allowed : 31.19 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.94 (0.39), residues: 515 helix: 2.20 (0.28), residues: 373 sheet: -3.35 (1.65), residues: 10 loop : -1.05 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 230 TYR 0.014 0.001 TYR A 275 PHE 0.011 0.001 PHE A 208 TRP 0.006 0.000 TRP A 285 HIS 0.001 0.000 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 3938) covalent geometry : angle 0.57966 ( 5387) SS BOND : bond 0.00065 ( 2) SS BOND : angle 0.27984 ( 4) hydrogen bonds : bond 0.04366 ( 264) hydrogen bonds : angle 3.94537 ( 771) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 ASP cc_start: 0.6927 (OUTLIER) cc_final: 0.6556 (p0) outliers start: 11 outliers final: 7 residues processed: 68 average time/residue: 0.8498 time to fit residues: 60.7851 Evaluate side-chains 63 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 32 CYS Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 518 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3360 r_free = 0.3360 target = 0.088811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.068939 restraints weight = 23255.664| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.60 r_work: 0.2881 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3940 Z= 0.126 Angle : 0.583 6.363 5391 Z= 0.295 Chirality : 0.035 0.122 642 Planarity : 0.005 0.059 678 Dihedral : 8.022 134.073 555 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.58 % Allowed : 31.96 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.98 (0.39), residues: 515 helix: 2.23 (0.28), residues: 373 sheet: -3.13 (1.66), residues: 10 loop : -1.05 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 230 TYR 0.014 0.001 TYR A 275 PHE 0.010 0.001 PHE A 208 TRP 0.005 0.001 TRP A 285 HIS 0.001 0.000 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 3938) covalent geometry : angle 0.58319 ( 5387) SS BOND : bond 0.00068 ( 2) SS BOND : angle 0.27771 ( 4) hydrogen bonds : bond 0.04252 ( 264) hydrogen bonds : angle 3.91899 ( 771) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 ASP cc_start: 0.6888 (OUTLIER) cc_final: 0.6534 (p0) outliers start: 10 outliers final: 8 residues processed: 65 average time/residue: 0.8597 time to fit residues: 58.7555 Evaluate side-chains 59 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 32 CYS Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 518 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 1 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.088974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.069194 restraints weight = 22796.377| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.58 r_work: 0.2881 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3940 Z= 0.129 Angle : 0.623 8.312 5391 Z= 0.312 Chirality : 0.035 0.121 642 Planarity : 0.004 0.038 678 Dihedral : 7.939 132.954 555 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.32 % Allowed : 32.99 % Favored : 64.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.00 (0.39), residues: 515 helix: 2.25 (0.28), residues: 373 sheet: -3.00 (1.71), residues: 10 loop : -1.09 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 203 TYR 0.013 0.001 TYR A 275 PHE 0.010 0.001 PHE A 360 TRP 0.005 0.000 TRP A 285 HIS 0.001 0.000 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3938) covalent geometry : angle 0.62353 ( 5387) SS BOND : bond 0.00073 ( 2) SS BOND : angle 0.25731 ( 4) hydrogen bonds : bond 0.04180 ( 264) hydrogen bonds : angle 3.87755 ( 771) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 ASP cc_start: 0.6871 (OUTLIER) cc_final: 0.6482 (p0) outliers start: 9 outliers final: 6 residues processed: 59 average time/residue: 0.7765 time to fit residues: 48.4243 Evaluate side-chains 61 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 32 CYS Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 518 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 49 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 10 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3365 r_free = 0.3365 target = 0.089402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.069393 restraints weight = 22746.682| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.57 r_work: 0.2887 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3940 Z= 0.129 Angle : 0.637 9.517 5391 Z= 0.316 Chirality : 0.035 0.120 642 Planarity : 0.004 0.038 678 Dihedral : 7.847 131.798 555 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.06 % Allowed : 33.51 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.04 (0.39), residues: 515 helix: 2.28 (0.28), residues: 373 sheet: -2.86 (1.73), residues: 10 loop : -1.06 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 230 TYR 0.013 0.001 TYR A 275 PHE 0.009 0.001 PHE A 360 TRP 0.005 0.001 TRP A 285 HIS 0.001 0.000 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3938) covalent geometry : angle 0.63700 ( 5387) SS BOND : bond 0.00069 ( 2) SS BOND : angle 0.31918 ( 4) hydrogen bonds : bond 0.04059 ( 264) hydrogen bonds : angle 3.82356 ( 771) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue VAL 330 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue LEU 464 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.7957 (tp30) cc_final: 0.7668 (mp0) REVERT: A 370 ASP cc_start: 0.6777 (OUTLIER) cc_final: 0.6466 (p0) outliers start: 8 outliers final: 8 residues processed: 60 average time/residue: 0.8508 time to fit residues: 53.6380 Evaluate side-chains 63 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 32 CYS Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 518 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 38 optimal weight: 0.0570 chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 5 optimal weight: 0.0370 chunk 36 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.089680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.070248 restraints weight = 22565.488| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.50 r_work: 0.2894 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.487 3940 Z= 0.339 Angle : 1.252 69.299 5391 Z= 0.510 Chirality : 0.109 2.590 642 Planarity : 0.005 0.038 678 Dihedral : 7.854 131.767 555 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.84 % Allowed : 32.99 % Favored : 64.18 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % 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: 2.04 (0.39), residues: 515 helix: 2.28 (0.28), residues: 373 sheet: -2.85 (1.73), residues: 10 loop : -1.09 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 230 TYR 0.013 0.001 TYR A 275 PHE 0.010 0.001 PHE A 360 TRP 0.005 0.000 TRP A 285 HIS 0.001 0.000 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00962 ( 3938) covalent geometry : angle 1.25241 ( 5387) SS BOND : bond 0.00040 ( 2) SS BOND : angle 0.29238 ( 4) hydrogen bonds : bond 0.04041 ( 264) hydrogen bonds : angle 3.81709 ( 771) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2516.73 seconds wall clock time: 43 minutes 26.00 seconds (2606.00 seconds total)