Starting phenix.real_space_refine on Sat May 2 09:34:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jki_61562/05_2026/9jki_61562_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jki_61562/05_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_61562/05_2026/9jki_61562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jki_61562/05_2026/9jki_61562.map" model { file = "/net/cci-nas-00/data/ceres_data/9jki_61562/05_2026/9jki_61562_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jki_61562/05_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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, 19 Unusual residues: {' NA': 2, '1XR': 1} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Time building chain proxies: 1.19, per 1000 atoms: 0.28 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: 0.42 Conformation dependent library (CDL) restraints added in 164.8 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: 0.22 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: 0.58 Time building geometry restraints manager: 0.51 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: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.970 Find NCS groups from input model: 0.010 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 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 covalent geometry : bond 0.00421 ( 4321) covalent geometry : angle 0.83312 ( 5900) SS BOND : bond 0.00055 ( 1) SS BOND : angle 0.26778 ( 2) hydrogen bonds : bond 0.19521 ( 173) hydrogen bonds : angle 7.84856 ( 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 : 0.125 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.4413 time to fit residues: 41.5545 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 : 0.143 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.6980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.161208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.127590 restraints weight = 4640.893| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.03 r_work: 0.3441 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1653 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= 0.147 Angle : 0.702 11.196 5902 Z= 0.365 Chirality : 0.044 0.289 667 Planarity : 0.005 0.042 722 Dihedral : 7.207 82.629 581 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.31 % Favored : 92.93 % Rotamer: Outliers : 2.26 % Allowed : 9.26 % Favored : 88.49 % 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: -2.52 (0.36), residues: 523 helix: -1.59 (0.26), residues: 359 sheet: None (None), residues: 0 loop : -1.42 (0.53), residues: 164 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 0.013 0.001 TRP A 617 HIS 0.002 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4321) covalent geometry : angle 0.70172 ( 5900) SS BOND : bond 0.00269 ( 1) SS BOND : angle 0.45432 ( 2) hydrogen bonds : bond 0.04196 ( 173) hydrogen bonds : angle 5.29773 ( 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 88 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.159 Fit side-chains REVERT: A 503 GLN cc_start: 0.6593 (tp40) cc_final: 0.6374 (tp-100) outliers start: 10 outliers final: 3 residues processed: 84 average time/residue: 0.4209 time to fit residues: 37.1026 Evaluate side-chains 62 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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: 0.6980 chunk 1 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3920 r_free = 0.3920 target = 0.160234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126202 restraints weight = 4612.620| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.99 r_work: 0.3423 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4322 Z= 0.141 Angle : 0.642 10.102 5902 Z= 0.333 Chirality : 0.043 0.226 667 Planarity : 0.004 0.044 722 Dihedral : 7.127 83.702 581 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.76 % Allowed : 5.74 % Favored : 93.50 % Rotamer: Outliers : 2.26 % Allowed : 12.64 % Favored : 85.10 % 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: -2.32 (0.36), residues: 523 helix: -1.32 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -1.67 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 85 TYR 0.010 0.001 TYR A 575 PHE 0.013 0.001 PHE A 504 TRP 0.016 0.001 TRP A 617 HIS 0.002 0.000 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 4321) covalent geometry : angle 0.64248 ( 5900) SS BOND : bond 0.00314 ( 1) SS BOND : angle 0.40113 ( 2) hydrogen bonds : bond 0.03996 ( 173) hydrogen bonds : angle 4.92836 ( 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 76 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.151 Fit side-chains REVERT: A 174 GLU cc_start: 0.7643 (mm-30) cc_final: 0.6958 (pt0) REVERT: A 181 ASN cc_start: 0.7344 (t0) cc_final: 0.6968 (m-40) REVERT: A 307 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.5974 (tm-30) REVERT: A 571 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7407 (mpp) REVERT: A 601 ARG cc_start: 0.6620 (tpt-90) cc_final: 0.6266 (tmt90) outliers start: 10 outliers final: 4 residues processed: 74 average time/residue: 0.3833 time to fit residues: 29.9235 Evaluate side-chains 65 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 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 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: 0.4980 chunk 22 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3864 r_free = 0.3864 target = 0.157010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122246 restraints weight = 4650.109| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.05 r_work: 0.3404 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4322 Z= 0.142 Angle : 0.625 9.260 5902 Z= 0.323 Chirality : 0.042 0.195 667 Planarity : 0.004 0.043 722 Dihedral : 7.037 82.080 581 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.88 % Favored : 92.35 % Rotamer: Outliers : 3.16 % Allowed : 13.32 % Favored : 83.52 % 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: -2.02 (0.36), residues: 523 helix: -1.02 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -1.74 (0.47), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 344 TYR 0.008 0.001 TYR A 548 PHE 0.012 0.001 PHE A 412 TRP 0.016 0.001 TRP A 617 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4321) covalent geometry : angle 0.62505 ( 5900) SS BOND : bond 0.00284 ( 1) SS BOND : angle 0.39445 ( 2) hydrogen bonds : bond 0.03905 ( 173) hydrogen bonds : angle 4.78944 ( 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 80 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.129 Fit side-chains REVERT: A 174 GLU cc_start: 0.7683 (mm-30) cc_final: 0.6925 (pt0) REVERT: A 181 ASN cc_start: 0.7357 (t0) cc_final: 0.6966 (m-40) REVERT: A 307 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.5857 (tm-30) REVERT: A 571 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7301 (mpp) REVERT: A 601 ARG cc_start: 0.6633 (tpt-90) cc_final: 0.6270 (tmt90) outliers start: 14 outliers final: 8 residues processed: 76 average time/residue: 0.3892 time to fit residues: 31.1128 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 409 VAL 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: 0.0050 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3927 r_free = 0.3927 target = 0.161525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127611 restraints weight = 4637.148| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.99 r_work: 0.3437 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2500 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= 0.114 Angle : 0.605 12.482 5902 Z= 0.309 Chirality : 0.041 0.202 667 Planarity : 0.004 0.041 722 Dihedral : 6.946 83.363 581 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.88 % Favored : 92.54 % Rotamer: Outliers : 2.26 % Allowed : 15.12 % Favored : 82.62 % 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: -1.59 (0.36), residues: 523 helix: -0.66 (0.28), residues: 354 sheet: None (None), residues: 0 loop : -1.67 (0.47), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 588 TYR 0.019 0.001 TYR A 519 PHE 0.009 0.001 PHE A 338 TRP 0.013 0.001 TRP A 617 HIS 0.002 0.000 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 4321) covalent geometry : angle 0.60552 ( 5900) SS BOND : bond 0.00170 ( 1) SS BOND : angle 0.24315 ( 2) hydrogen bonds : bond 0.03558 ( 173) hydrogen bonds : angle 4.61407 ( 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 76 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.164 Fit side-chains REVERT: A 174 GLU cc_start: 0.7656 (mm-30) cc_final: 0.6937 (pt0) REVERT: A 181 ASN cc_start: 0.7344 (t0) cc_final: 0.6950 (m-40) REVERT: A 307 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.5857 (tm-30) REVERT: A 571 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7186 (mpp) REVERT: A 601 ARG cc_start: 0.6602 (tpt-90) cc_final: 0.6196 (tmt90) outliers start: 10 outliers final: 8 residues processed: 71 average time/residue: 0.3920 time to fit residues: 29.4473 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 : 0.149 ------------------------------------------------------------------------------- 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 462 PHE 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: 0.6980 chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3915 r_free = 0.3915 target = 0.160257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.126053 restraints weight = 4734.896| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.00 r_work: 0.3409 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4322 Z= 0.140 Angle : 0.633 11.975 5902 Z= 0.319 Chirality : 0.043 0.209 667 Planarity : 0.004 0.041 722 Dihedral : 6.915 81.483 581 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.88 % Favored : 92.54 % Rotamer: Outliers : 2.93 % Allowed : 16.03 % Favored : 81.04 % 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: -1.42 (0.36), residues: 523 helix: -0.56 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -1.53 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 237 TYR 0.014 0.001 TYR A 575 PHE 0.012 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 covalent geometry : bond 0.00324 ( 4321) covalent geometry : angle 0.63266 ( 5900) SS BOND : bond 0.00184 ( 1) SS BOND : angle 0.24011 ( 2) hydrogen bonds : bond 0.03799 ( 173) hydrogen bonds : angle 4.65646 ( 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 77 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.136 Fit side-chains REVERT: A 174 GLU cc_start: 0.7635 (mm-30) cc_final: 0.6927 (pt0) REVERT: A 181 ASN cc_start: 0.7385 (t0) cc_final: 0.6966 (m-40) REVERT: A 307 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.5824 (tm-30) REVERT: A 571 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7260 (mpp) REVERT: A 601 ARG cc_start: 0.6594 (tpt-90) cc_final: 0.6192 (tmt90) outliers start: 13 outliers final: 11 residues processed: 71 average time/residue: 0.3666 time to fit residues: 27.5403 Evaluate side-chains 75 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 215 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 287 LEU 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 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: 0.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 18 optimal weight: 0.0270 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3907 r_free = 0.3907 target = 0.158685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.123861 restraints weight = 4691.123| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.09 r_work: 0.3398 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2685 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= 0.128 Angle : 0.629 11.843 5902 Z= 0.316 Chirality : 0.044 0.282 667 Planarity : 0.004 0.040 722 Dihedral : 6.875 82.253 581 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.69 % Favored : 92.73 % Rotamer: Outliers : 2.93 % Allowed : 16.70 % Favored : 80.36 % 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 are not related in a simple way. whole: -1.27 (0.37), residues: 523 helix: -0.43 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -1.50 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 237 TYR 0.020 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 covalent geometry : bond 0.00289 ( 4321) covalent geometry : angle 0.62936 ( 5900) SS BOND : bond 0.00173 ( 1) SS BOND : angle 0.18809 ( 2) hydrogen bonds : bond 0.03723 ( 173) hydrogen bonds : angle 4.60305 ( 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 77 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.159 Fit side-chains REVERT: A 181 ASN cc_start: 0.7490 (t0) cc_final: 0.7054 (m-40) REVERT: A 307 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.5729 (tm-30) REVERT: A 571 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7217 (mpp) REVERT: A 601 ARG cc_start: 0.6609 (tpt-90) cc_final: 0.6304 (tmt90) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.3603 time to fit residues: 27.4676 Evaluate side-chains 74 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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 215 GLU Chi-restraints excluded: chain A residue 287 LEU 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 462 PHE Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 571 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 26 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 44 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 36 optimal weight: 0.5980 chunk 48 optimal weight: 0.0050 chunk 47 optimal weight: 4.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3932 r_free = 0.3932 target = 0.161108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.126811 restraints weight = 4594.497| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.07 r_work: 0.3434 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4322 Z= 0.109 Angle : 0.608 11.722 5902 Z= 0.304 Chirality : 0.042 0.253 667 Planarity : 0.004 0.039 722 Dihedral : 6.786 83.514 581 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.31 % Favored : 93.12 % Rotamer: Outliers : 2.26 % Allowed : 17.38 % Favored : 80.36 % 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 are not related in a simple way. whole: -0.96 (0.37), residues: 523 helix: -0.23 (0.28), residues: 359 sheet: None (None), residues: 0 loop : -1.31 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 588 TYR 0.011 0.001 TYR A 575 PHE 0.009 0.001 PHE A 98 TRP 0.013 0.001 TRP A 556 HIS 0.002 0.000 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 4321) covalent geometry : angle 0.60770 ( 5900) SS BOND : bond 0.00169 ( 1) SS BOND : angle 0.15307 ( 2) hydrogen bonds : bond 0.03471 ( 173) hydrogen bonds : angle 4.52840 ( 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 75 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.165 Fit side-chains REVERT: A 106 MET cc_start: 0.8441 (tpp) cc_final: 0.8157 (tpp) REVERT: A 181 ASN cc_start: 0.7421 (t0) cc_final: 0.6990 (m-40) REVERT: A 307 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.5707 (tm-30) REVERT: A 571 MET cc_start: 0.7810 (mpp) cc_final: 0.7202 (mpp) REVERT: A 601 ARG cc_start: 0.6590 (tpt-90) cc_final: 0.6290 (tmt90) outliers start: 10 outliers final: 9 residues processed: 70 average time/residue: 0.3610 time to fit residues: 26.7778 Evaluate side-chains 74 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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 215 GLU Chi-restraints excluded: chain A residue 287 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 48 optimal weight: 0.3980 chunk 39 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.0050 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.160636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.125999 restraints weight = 4673.078| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.08 r_work: 0.3427 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4322 Z= 0.116 Angle : 0.618 11.671 5902 Z= 0.307 Chirality : 0.043 0.267 667 Planarity : 0.004 0.039 722 Dihedral : 6.731 83.016 581 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.69 % Favored : 92.73 % Rotamer: Outliers : 3.16 % Allowed : 17.16 % 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: -0.83 (0.38), residues: 523 helix: -0.14 (0.28), residues: 359 sheet: None (None), residues: 0 loop : -1.23 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.021 0.001 TYR A 519 PHE 0.009 0.001 PHE A 412 TRP 0.016 0.001 TRP A 556 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 4321) covalent geometry : angle 0.61781 ( 5900) SS BOND : bond 0.00152 ( 1) SS BOND : angle 0.14494 ( 2) hydrogen bonds : bond 0.03591 ( 173) hydrogen bonds : angle 4.51077 ( 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 79 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 ASN cc_start: 0.7455 (t0) cc_final: 0.7029 (m-40) REVERT: A 307 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.5690 (tm-30) REVERT: A 571 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7211 (mpp) outliers start: 14 outliers final: 11 residues processed: 73 average time/residue: 0.2864 time to fit residues: 22.2748 Evaluate side-chains 75 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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 215 GLU Chi-restraints excluded: chain A residue 287 LEU 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 462 PHE 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: 3.9990 chunk 34 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 18 optimal weight: 0.0040 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.160224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.125643 restraints weight = 4571.772| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.08 r_work: 0.3421 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2913 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= 0.122 Angle : 0.626 11.594 5902 Z= 0.313 Chirality : 0.043 0.253 667 Planarity : 0.004 0.039 722 Dihedral : 6.730 82.922 581 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.69 % Favored : 92.73 % Rotamer: Outliers : 2.71 % Allowed : 17.38 % 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: -0.79 (0.38), residues: 523 helix: -0.11 (0.28), residues: 359 sheet: None (None), residues: 0 loop : -1.21 (0.50), residues: 164 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 0.017 0.001 TRP A 556 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4321) covalent geometry : angle 0.62639 ( 5900) SS BOND : bond 0.00161 ( 1) SS BOND : angle 0.19158 ( 2) hydrogen bonds : bond 0.03682 ( 173) hydrogen bonds : angle 4.51554 ( 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 77 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.097 Fit side-chains revert: symmetry clash REVERT: A 106 MET cc_start: 0.8457 (tpp) cc_final: 0.8173 (tpp) REVERT: A 181 ASN cc_start: 0.7425 (t0) cc_final: 0.7003 (m-40) REVERT: A 307 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.5606 (tm-30) REVERT: A 571 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7212 (mpp) outliers start: 12 outliers final: 11 residues processed: 71 average time/residue: 0.2531 time to fit residues: 19.0814 Evaluate side-chains 75 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.089 ------------------------------------------------------------------------------- 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 215 GLU Chi-restraints excluded: chain A residue 287 LEU 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 462 PHE 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: 7.9990 chunk 34 optimal weight: 0.0270 chunk 51 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 21 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3931 r_free = 0.3931 target = 0.161172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.126292 restraints weight = 4620.397| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.09 r_work: 0.3427 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2986 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= 0.116 Angle : 0.625 11.437 5902 Z= 0.313 Chirality : 0.043 0.255 667 Planarity : 0.004 0.039 722 Dihedral : 6.705 83.487 581 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.31 % Favored : 93.12 % Rotamer: Outliers : 2.71 % Allowed : 17.61 % 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 (0.38), residues: 523 helix: -0.04 (0.28), residues: 359 sheet: None (None), residues: 0 loop : -1.16 (0.50), residues: 164 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 0.009 0.001 PHE A 412 TRP 0.017 0.001 TRP A 556 HIS 0.002 0.001 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 4321) covalent geometry : angle 0.62509 ( 5900) SS BOND : bond 0.00152 ( 1) SS BOND : angle 0.17500 ( 2) hydrogen bonds : bond 0.03567 ( 173) hydrogen bonds : angle 4.48049 ( 492) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1722.67 seconds wall clock time: 30 minutes 1.58 seconds (1801.58 seconds total)