Starting phenix.real_space_refine on Wed Jul 1 23:45:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jki_61562/07_2026/9jki_61562_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jki_61562/07_2026/9jki_61562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jki_61562/07_2026/9jki_61562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jki_61562/07_2026/9jki_61562.map" model { file = "/net/cci-nas-00/data/ceres_data/9jki_61562/07_2026/9jki_61562_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jki_61562/07_2026/9jki_61562_trim.cif" } resolution = 2.69 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= -0.002 sd= 0.076 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 S 23 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2799 2.51 5 N 659 2.21 5 O 710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4194 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4175 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 505} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'1XR': 1} Classifications: {'undetermined': 1, 'water': 1} Chain breaks: 2 Time building chain proxies: 0.73, per 1000 atoms: 0.17 Number of scatterers: 4194 At special positions: 0 Unit cell: (75.0537, 64.9341, 86.0166, 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) Cl 1 17.00 S 23 16.00 Na 2 11.00 O 710 8.00 N 659 7.00 C 2799 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 189 " 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: 0.22 Conformation dependent library (CDL) restraints added in 94.9 milliseconds 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 974 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 1 sheets defined 61.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 68 through 71 removed outlier: 3.501A pdb=" N LEU A 71 " --> pdb=" O ASP A 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 68 through 71' Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 84 through 94 removed outlier: 3.637A pdb=" N TYR A 88 " --> pdb=" O TRP A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 125 removed outlier: 3.505A pdb=" N GLU A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 removed outlier: 4.246A pdb=" N ILE A 134 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 169 removed outlier: 3.597A pdb=" N VAL A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N VAL A 158 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 274 through 286 removed outlier: 3.505A pdb=" N THR A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 removed outlier: 3.741A pdb=" N GLY A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 323 removed outlier: 3.506A pdb=" N THR A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.852A pdb=" N ALA A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 352 removed outlier: 3.717A pdb=" N ASP A 345 " --> pdb=" O ASN A 341 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 347 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 368 removed outlier: 3.593A pdb=" N SER A 357 " --> pdb=" O ASN A 353 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 399 Proline residue: A 395 - end of helix removed outlier: 3.742A pdb=" N ALA A 399 " --> pdb=" O PRO A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 438 removed outlier: 3.598A pdb=" N GLU A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.961A pdb=" N ARG A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HIS A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 439 through 444' Processing helix chain 'A' and resid 444 through 462 removed outlier: 3.687A pdb=" N THR A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 467 through 479 removed outlier: 3.649A pdb=" N VAL A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 497 Processing helix chain 'A' and resid 500 through 513 Processing helix chain 'A' and resid 526 through 542 removed outlier: 3.764A pdb=" N PHE A 534 " --> pdb=" O CYS A 530 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE A 540 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 561 through 569 removed outlier: 4.372A pdb=" N SER A 567 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 579 removed outlier: 3.617A pdb=" N ALA A 577 " --> pdb=" O PRO A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 601 Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.916A pdb=" N THR A 613 " --> pdb=" O ARG A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 619 removed outlier: 3.723A pdb=" N LEU A 618 " --> pdb=" O ARG A 615 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 619 " --> pdb=" O HIS A 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 615 through 619' Processing sheet with id=AA1, first strand: chain 'A' and resid 547 through 548 173 hydrogen bonds defined for protein. 492 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: 0.44 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 624 1.29 - 1.42: 1272 1.42 - 1.55: 2389 1.55 - 1.68: 1 1.68 - 1.81: 35 Bond restraints: 4321 Sorted by residual: bond pdb=" C ASP A 79 " pdb=" O ASP A 79 " ideal model delta sigma weight residual 1.235 1.160 0.075 1.02e-02 9.61e+03 5.38e+01 bond pdb=" N ASP A 79 " pdb=" CA ASP A 79 " ideal model delta sigma weight residual 1.459 1.390 0.070 1.19e-02 7.06e+03 3.42e+01 bond pdb=" N ASN A 82 " pdb=" CA ASN A 82 " ideal model delta sigma weight residual 1.458 1.384 0.073 1.35e-02 5.49e+03 2.93e+01 bond pdb=" CA ASN A 82 " pdb=" C ASN A 82 " ideal model delta sigma weight residual 1.519 1.473 0.046 1.19e-02 7.06e+03 1.48e+01 bond pdb=" CA ASP A 79 " pdb=" C ASP A 79 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.25e-02 6.40e+03 1.20e+01 ... (remaining 4316 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 5660 1.94 - 3.88: 200 3.88 - 5.82: 32 5.82 - 7.76: 5 7.76 - 9.70: 3 Bond angle restraints: 5900 Sorted by residual: angle pdb=" N ASN A 82 " pdb=" CA ASN A 82 " pdb=" C ASN A 82 " ideal model delta sigma weight residual 113.43 103.73 9.70 1.26e+00 6.30e-01 5.92e+01 angle pdb=" N VAL A 247 " pdb=" CA VAL A 247 " pdb=" C VAL A 247 " ideal model delta sigma weight residual 111.56 106.56 5.00 8.60e-01 1.35e+00 3.38e+01 angle pdb=" N VAL A 563 " pdb=" CA VAL A 563 " pdb=" C VAL A 563 " ideal model delta sigma weight residual 112.29 107.38 4.91 9.40e-01 1.13e+00 2.73e+01 angle pdb=" N ILE A 564 " pdb=" CA ILE A 564 " pdb=" C ILE A 564 " ideal model delta sigma weight residual 113.42 107.82 5.60 1.17e+00 7.31e-01 2.29e+01 angle pdb=" C ASN A 82 " pdb=" N VAL A 83 " pdb=" CA VAL A 83 " ideal model delta sigma weight residual 121.34 129.08 -7.74 1.62e+00 3.81e-01 2.28e+01 ... (remaining 5895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 2240 17.14 - 34.28: 173 34.28 - 51.41: 23 51.41 - 68.55: 1 68.55 - 85.69: 5 Dihedral angle restraints: 2442 sinusoidal: 918 harmonic: 1524 Sorted by residual: dihedral pdb=" CA ILE A 67 " pdb=" C ILE A 67 " pdb=" N ASP A 68 " pdb=" CA ASP A 68 " ideal model delta harmonic sigma weight residual 180.00 147.67 32.33 0 5.00e+00 4.00e-02 4.18e+01 dihedral pdb=" CA LEU A 522 " pdb=" C LEU A 522 " pdb=" N CYS A 523 " pdb=" CA CYS A 523 " ideal model delta harmonic sigma weight residual 180.00 159.68 20.32 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" N ASN A 82 " pdb=" C ASN A 82 " pdb=" CA ASN A 82 " pdb=" CB ASN A 82 " ideal model delta harmonic sigma weight residual 122.80 113.72 9.08 0 2.50e+00 1.60e-01 1.32e+01 ... (remaining 2439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 430 0.034 - 0.067: 186 0.067 - 0.101: 37 0.101 - 0.135: 12 0.135 - 0.169: 2 Chirality restraints: 667 Sorted by residual: chirality pdb=" C2 1XR A 701 " pdb=" C1 1XR A 701 " pdb=" C3 1XR A 701 " pdb=" N1 1XR A 701 " both_signs ideal model delta sigma weight residual False -2.43 -2.59 0.17 2.00e-01 2.50e+01 7.10e-01 chirality pdb=" CB ILE A 67 " pdb=" CA ILE A 67 " pdb=" CG1 ILE A 67 " pdb=" CG2 ILE A 67 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CA VAL A 247 " pdb=" N VAL A 247 " pdb=" C VAL A 247 " pdb=" CB VAL A 247 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 664 not shown) Planarity restraints: 722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 80 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.74e+00 pdb=" C LEU A 80 " 0.041 2.00e-02 2.50e+03 pdb=" O LEU A 80 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA A 81 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 81 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C ALA A 81 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA A 81 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN A 82 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 79 " 0.009 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" CG ASP A 79 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASP A 79 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP A 79 " 0.012 2.00e-02 2.50e+03 ... (remaining 719 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 64 2.64 - 3.20: 4068 3.20 - 3.77: 6512 3.77 - 4.33: 9911 4.33 - 4.90: 15704 Nonbonded interactions: 36259 Sorted by model distance: nonbonded pdb=" OH TYR A 499 " pdb=" OD2 ASP A 507 " model vdw 2.073 3.040 nonbonded pdb=" O ARG A 237 " pdb=" OG1 THR A 241 " model vdw 2.162 3.040 nonbonded pdb=" O TYR A 274 " pdb=" OG1 THR A 278 " model vdw 2.178 3.040 nonbonded pdb=" OH TYR A 252 " pdb=" O GLU A 446 " model vdw 2.202 3.040 nonbonded pdb=" OG SER A 227 " pdb=" O ASP A 232 " model vdw 2.212 3.040 ... (remaining 36254 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.970 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 0.075 4322 Z= 0.280 Angle : 0.833 9.696 5902 Z= 0.557 Chirality : 0.039 0.169 667 Planarity : 0.004 0.031 722 Dihedral : 12.518 85.688 1465 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 35.17 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.84 % Favored : 91.40 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 are not related in a simple way. whole: -2.88 (0.37), residues: 523 helix: -1.78 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -1.82 (0.51), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 588 TYR 0.012 0.001 TYR A 115 PHE 0.007 0.001 PHE A 365 TRP 0.016 0.001 TRP A 617 HIS 0.002 0.000 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.28 ( 4321) covalent geometry : angle 0.83312 / 0.56 ( 5900) SS BOND : bond 0.00055 / 0.03 ( 1) SS BOND : angle 0.26778 / 0.15 ( 2) hydrogen bonds : bond 0.19521 / 12.76 ( 173) hydrogen bonds : angle 7.84856 / 5.26 ( 492) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.196 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.3530 time to fit residues: 33.3359 Evaluate side-chains 67 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS A 353 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.157516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123638 restraints weight = 4695.962| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.04 r_work: 0.3436 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4322 Z= 0.149 Angle : 0.705 11.238 5902 Z= 0.367 Chirality : 0.044 0.287 667 Planarity : 0.005 0.043 722 Dihedral : 7.222 83.179 581 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.31 % Favored : 92.93 % Rotamer: Outliers : 2.26 % Allowed : 9.03 % Favored : 88.71 % 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 are not related in a simple way. whole: -2.54 (0.36), residues: 523 helix: -1.62 (0.26), residues: 360 sheet: None (None), residues: 0 loop : -1.40 (0.53), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 219 TYR 0.012 0.001 TYR A 575 PHE 0.018 0.002 PHE A 338 TRP 0.014 0.001 TRP A 617 HIS 0.002 0.001 HIS A 616 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 4321) covalent geometry : angle 0.70517 / 0.37 ( 5900) SS BOND : bond 0.00307 / 0.16 ( 1) SS BOND : angle 0.45960 / 0.26 ( 2) hydrogen bonds : bond 0.04215 / 2.84 ( 173) hydrogen bonds : angle 5.29370 / 3.58 ( 492) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.107 Fit side-chains REVERT: A 336 ASN cc_start: 0.8762 (m110) cc_final: 0.8433 (m110) REVERT: A 503 GLN cc_start: 0.6597 (tp40) cc_final: 0.6375 (tp-100) outliers start: 10 outliers final: 3 residues processed: 85 average time/residue: 0.2995 time to fit residues: 26.8962 Evaluate side-chains 64 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 620 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 0.0980 chunk 42 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS A 514 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.161874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.127403 restraints weight = 4601.269| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.05 r_work: 0.3438 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4322 Z= 0.125 Angle : 0.627 10.043 5902 Z= 0.325 Chirality : 0.042 0.227 667 Planarity : 0.004 0.043 722 Dihedral : 7.114 85.546 581 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.76 % Allowed : 5.74 % Favored : 93.50 % Rotamer: Outliers : 1.81 % Allowed : 12.64 % Favored : 85.55 % 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 are not related in a simple way. whole: -2.24 (0.36), residues: 523 helix: -1.25 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -1.68 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.009 0.001 TYR A 575 PHE 0.013 0.001 PHE A 478 TRP 0.015 0.001 TRP A 617 HIS 0.002 0.000 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 4321) covalent geometry : angle 0.62696 / 0.32 ( 5900) SS BOND : bond 0.00307 / 0.16 ( 1) SS BOND : angle 0.42764 / 0.25 ( 2) hydrogen bonds : bond 0.03795 / 2.59 ( 173) hydrogen bonds : angle 4.88438 / 3.32 ( 492) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.146 Fit side-chains REVERT: A 174 GLU cc_start: 0.7706 (mm-30) cc_final: 0.6940 (pt0) REVERT: A 181 ASN cc_start: 0.7288 (t0) cc_final: 0.6906 (m-40) REVERT: A 307 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.5921 (tm-30) REVERT: A 336 ASN cc_start: 0.8737 (m110) cc_final: 0.8418 (m110) REVERT: A 571 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7398 (mpp) REVERT: A 601 ARG cc_start: 0.6603 (tpt-90) cc_final: 0.6238 (tmt90) outliers start: 8 outliers final: 5 residues processed: 75 average time/residue: 0.2779 time to fit residues: 22.0613 Evaluate side-chains 68 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 571 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 20 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.158338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.123839 restraints weight = 4644.459| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.04 r_work: 0.3421 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4322 Z= 0.132 Angle : 0.614 9.197 5902 Z= 0.317 Chirality : 0.042 0.197 667 Planarity : 0.004 0.043 722 Dihedral : 7.019 84.138 581 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.31 % Favored : 92.93 % Rotamer: Outliers : 2.03 % Allowed : 14.22 % Favored : 83.75 % 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 are not related in a simple way. whole: -1.97 (0.36), residues: 523 helix: -0.94 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -1.82 (0.46), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 344 TYR 0.008 0.001 TYR A 115 PHE 0.011 0.001 PHE A 412 TRP 0.014 0.001 TRP A 617 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 4321) covalent geometry : angle 0.61367 / 0.32 ( 5900) SS BOND : bond 0.00225 / 0.12 ( 1) SS BOND : angle 0.30266 / 0.18 ( 2) hydrogen bonds : bond 0.03774 / 2.58 ( 173) hydrogen bonds : angle 4.76460 / 3.24 ( 492) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.096 Fit side-chains revert: symmetry clash REVERT: A 174 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7018 (pt0) REVERT: A 181 ASN cc_start: 0.7304 (t0) cc_final: 0.6923 (m-40) REVERT: A 307 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.5878 (tm-30) REVERT: A 571 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7281 (mpp) REVERT: A 601 ARG cc_start: 0.6607 (tpt-90) cc_final: 0.6230 (tmt90) outliers start: 9 outliers final: 6 residues processed: 73 average time/residue: 0.2968 time to fit residues: 22.8597 Evaluate side-chains 71 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 571 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.157572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.123547 restraints weight = 4693.720| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.03 r_work: 0.3420 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4322 Z= 0.126 Angle : 0.612 12.401 5902 Z= 0.313 Chirality : 0.042 0.195 667 Planarity : 0.004 0.041 722 Dihedral : 6.960 84.056 581 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.88 % Favored : 92.54 % Rotamer: Outliers : 2.26 % Allowed : 14.90 % Favored : 82.84 % 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 are not related in a simple way. whole: -1.67 (0.36), residues: 523 helix: -0.76 (0.27), residues: 357 sheet: None (None), residues: 0 loop : -1.61 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 588 TYR 0.018 0.001 TYR A 519 PHE 0.011 0.001 PHE A 412 TRP 0.013 0.001 TRP A 617 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 4321) covalent geometry : angle 0.61186 / 0.31 ( 5900) SS BOND : bond 0.00207 / 0.11 ( 1) SS BOND : angle 0.33452 / 0.20 ( 2) hydrogen bonds : bond 0.03651 / 2.48 ( 173) hydrogen bonds : angle 4.66070 / 3.17 ( 492) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.115 Fit side-chains REVERT: A 174 GLU cc_start: 0.7710 (mm-30) cc_final: 0.6955 (pt0) REVERT: A 181 ASN cc_start: 0.7321 (t0) cc_final: 0.6939 (m-40) REVERT: A 307 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.5872 (tm-30) REVERT: A 571 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7237 (mpp) REVERT: A 601 ARG cc_start: 0.6595 (tpt-90) cc_final: 0.6196 (tmt90) outliers start: 10 outliers final: 7 residues processed: 69 average time/residue: 0.2890 time to fit residues: 21.1431 Evaluate side-chains 68 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 571 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 0.0970 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.160972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.126585 restraints weight = 4710.948| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.09 r_work: 0.3436 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4322 Z= 0.109 Angle : 0.590 11.829 5902 Z= 0.301 Chirality : 0.041 0.212 667 Planarity : 0.004 0.039 722 Dihedral : 6.839 85.143 581 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.88 % Favored : 92.54 % Rotamer: Outliers : 2.26 % Allowed : 16.25 % Favored : 81.49 % 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 are not related in a simple way. whole: -1.30 (0.37), residues: 523 helix: -0.50 (0.28), residues: 359 sheet: None (None), residues: 0 loop : -1.42 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 588 TYR 0.009 0.001 TYR A 156 PHE 0.009 0.001 PHE A 98 TRP 0.012 0.001 TRP A 556 HIS 0.001 0.000 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 4321) covalent geometry : angle 0.59038 / 0.30 ( 5900) SS BOND : bond 0.00198 / 0.10 ( 1) SS BOND : angle 0.25541 / 0.15 ( 2) hydrogen bonds : bond 0.03412 / 2.30 ( 173) hydrogen bonds : angle 4.53407 / 3.10 ( 492) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: A 181 ASN cc_start: 0.7418 (t0) cc_final: 0.7001 (m-40) REVERT: A 307 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.5699 (tm-30) REVERT: A 571 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7197 (mpp) REVERT: A 601 ARG cc_start: 0.6625 (tpt-90) cc_final: 0.6335 (tmt90) outliers start: 10 outliers final: 7 residues processed: 72 average time/residue: 0.2667 time to fit residues: 20.3694 Evaluate side-chains 71 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 571 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 50 optimal weight: 0.7980 chunk 11 optimal weight: 0.0050 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 24 optimal weight: 0.0370 chunk 44 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 18 optimal weight: 0.0030 overall best weight: 0.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.163185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.129799 restraints weight = 4676.982| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.04 r_work: 0.3477 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4322 Z= 0.098 Angle : 0.578 11.646 5902 Z= 0.290 Chirality : 0.041 0.213 667 Planarity : 0.004 0.037 722 Dihedral : 6.714 86.055 581 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.12 % Favored : 93.31 % Rotamer: Outliers : 2.48 % Allowed : 16.03 % Favored : 81.49 % 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 are not related in a simple way. whole: -1.05 (0.37), residues: 523 helix: -0.34 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -1.24 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 283 TYR 0.019 0.001 TYR A 519 PHE 0.008 0.001 PHE A 338 TRP 0.015 0.001 TRP A 556 HIS 0.001 0.000 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 ( 4321) covalent geometry : angle 0.57854 / 0.29 ( 5900) SS BOND : bond 0.00178 / 0.09 ( 1) SS BOND : angle 0.27744 / 0.16 ( 2) hydrogen bonds : bond 0.03181 / 2.14 ( 173) hydrogen bonds : angle 4.43832 / 3.04 ( 492) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.151 Fit side-chains REVERT: A 106 MET cc_start: 0.8422 (tpp) cc_final: 0.8145 (tpp) REVERT: A 181 ASN cc_start: 0.7332 (t0) cc_final: 0.6968 (m-40) REVERT: A 299 SER cc_start: 0.8418 (OUTLIER) cc_final: 0.8153 (p) REVERT: A 307 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.5686 (tm-30) REVERT: A 336 ASN cc_start: 0.8617 (m110) cc_final: 0.8361 (m110) REVERT: A 571 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7174 (mpp) REVERT: A 618 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7549 (tp) outliers start: 11 outliers final: 5 residues processed: 76 average time/residue: 0.2649 time to fit residues: 21.4195 Evaluate side-chains 67 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 618 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 26 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 37 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 0.0040 chunk 36 optimal weight: 0.4980 chunk 48 optimal weight: 0.0000 chunk 47 optimal weight: 3.9990 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.164577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.130254 restraints weight = 4570.269| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.07 r_work: 0.3482 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 4322 Z= 0.102 Angle : 0.616 11.713 5902 Z= 0.300 Chirality : 0.041 0.217 667 Planarity : 0.004 0.036 722 Dihedral : 6.626 86.045 581 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.50 % Favored : 92.93 % Rotamer: Outliers : 2.03 % Allowed : 18.28 % Favored : 79.68 % 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 are not related in a simple way. whole: -0.80 (0.38), residues: 523 helix: -0.17 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.14 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 588 TYR 0.010 0.001 TYR A 575 PHE 0.008 0.001 PHE A 338 TRP 0.016 0.001 TRP A 556 HIS 0.003 0.000 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 4321) covalent geometry : angle 0.61648 / 0.30 ( 5900) SS BOND : bond 0.00152 / 0.08 ( 1) SS BOND : angle 0.17100 / 0.10 ( 2) hydrogen bonds : bond 0.03146 / 2.10 ( 173) hydrogen bonds : angle 4.40802 / 3.03 ( 492) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: A 106 MET cc_start: 0.8391 (tpp) cc_final: 0.8128 (tpp) REVERT: A 181 ASN cc_start: 0.7323 (t0) cc_final: 0.6963 (m-40) REVERT: A 307 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.5682 (tm-30) REVERT: A 336 ASN cc_start: 0.8554 (m110) cc_final: 0.8317 (m110) REVERT: A 571 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7178 (mpp) REVERT: A 618 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7536 (tp) outliers start: 9 outliers final: 6 residues processed: 66 average time/residue: 0.2854 time to fit residues: 20.0429 Evaluate side-chains 68 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 618 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.158332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.123302 restraints weight = 4688.736| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.10 r_work: 0.3389 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4322 Z= 0.161 Angle : 0.681 11.850 5902 Z= 0.335 Chirality : 0.045 0.269 667 Planarity : 0.004 0.038 722 Dihedral : 6.747 82.979 581 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.69 % Favored : 92.73 % Rotamer: Outliers : 2.03 % Allowed : 18.51 % Favored : 79.46 % 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 are not related in a simple way. whole: -1.00 (0.37), residues: 523 helix: -0.24 (0.28), residues: 358 sheet: None (None), residues: 0 loop : -1.38 (0.49), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.019 0.001 TYR A 519 PHE 0.015 0.001 PHE A 412 TRP 0.018 0.002 TRP A 556 HIS 0.003 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 4321) covalent geometry : angle 0.68093 / 0.34 ( 5900) SS BOND : bond 0.00189 / 0.10 ( 1) SS BOND : angle 0.27971 / 0.15 ( 2) hydrogen bonds : bond 0.03938 / 2.67 ( 173) hydrogen bonds : angle 4.60732 / 3.14 ( 492) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 ASN cc_start: 0.7459 (t0) cc_final: 0.7066 (m-40) REVERT: A 307 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.5637 (tm-30) REVERT: A 571 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7239 (mpp) outliers start: 9 outliers final: 8 residues processed: 66 average time/residue: 0.3165 time to fit residues: 22.2874 Evaluate side-chains 72 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 618 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 3 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.160731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.126283 restraints weight = 4571.568| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.08 r_work: 0.3429 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4322 Z= 0.115 Angle : 0.638 11.503 5902 Z= 0.313 Chirality : 0.043 0.279 667 Planarity : 0.004 0.037 722 Dihedral : 6.699 84.832 581 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.31 % Favored : 93.12 % Rotamer: Outliers : 2.03 % Allowed : 18.06 % Favored : 79.91 % 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 are not related in a simple way. whole: -0.76 (0.38), residues: 523 helix: -0.10 (0.28), residues: 360 sheet: None (None), residues: 0 loop : -1.19 (0.50), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.011 0.001 TYR A 575 PHE 0.010 0.001 PHE A 412 TRP 0.019 0.001 TRP A 556 HIS 0.003 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 4321) covalent geometry : angle 0.63851 / 0.31 ( 5900) SS BOND : bond 0.00172 / 0.09 ( 1) SS BOND : angle 0.24320 / 0.14 ( 2) hydrogen bonds : bond 0.03532 / 2.38 ( 173) hydrogen bonds : angle 4.55350 / 3.10 ( 492) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 174 GLU cc_start: 0.7882 (tp30) cc_final: 0.7644 (mm-30) REVERT: A 181 ASN cc_start: 0.7397 (t0) cc_final: 0.7023 (m110) REVERT: A 307 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.5578 (tm-30) REVERT: A 571 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7208 (mpp) outliers start: 9 outliers final: 8 residues processed: 67 average time/residue: 0.3051 time to fit residues: 21.7813 Evaluate side-chains 72 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 618 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 46 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.160220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.125374 restraints weight = 4634.612| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.09 r_work: 0.3416 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4322 Z= 0.123 Angle : 0.646 11.507 5902 Z= 0.317 Chirality : 0.043 0.261 667 Planarity : 0.004 0.037 722 Dihedral : 6.655 84.298 581 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.12 % Favored : 93.31 % Rotamer: Outliers : 2.48 % Allowed : 17.83 % Favored : 79.68 % 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 are not related in a simple way. whole: -0.69 (0.37), residues: 523 helix: -0.05 (0.28), residues: 360 sheet: None (None), residues: 0 loop : -1.15 (0.50), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.023 0.001 TYR A 519 PHE 0.011 0.001 PHE A 412 TRP 0.019 0.001 TRP A 556 HIS 0.003 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 4321) covalent geometry : angle 0.64612 / 0.32 ( 5900) SS BOND : bond 0.00174 / 0.09 ( 1) SS BOND : angle 0.24509 / 0.14 ( 2) hydrogen bonds : bond 0.03629 / 2.47 ( 173) hydrogen bonds : angle 4.54306 / 3.09 ( 492) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1474.94 seconds wall clock time: 25 minutes 51.05 seconds (1551.05 seconds total)