Starting phenix.real_space_refine on Thu Jul 2 02:30:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kmm_62438/07_2026/9kmm_62438.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kmm_62438/07_2026/9kmm_62438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kmm_62438/07_2026/9kmm_62438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kmm_62438/07_2026/9kmm_62438.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kmm_62438/07_2026/9kmm_62438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kmm_62438/07_2026/9kmm_62438.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 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 41 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 3892 2.51 5 N 940 2.21 5 O 1055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 5931 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 922 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "A" Number of atoms: 4193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4193 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 804 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 9 Ad-hoc single atom residues: {' CL': 1, ' NA': 2} Unusual residues: {'IZC': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Time building chain proxies: 1.06, per 1000 atoms: 0.18 Number of scatterers: 5931 At special positions: 0 Unit cell: (72.98, 82.82, 112.34, 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 41 16.00 Na 2 11.00 O 1055 8.00 N 940 7.00 C 3892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " 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: 0.34 Conformation dependent library (CDL) restraints added in 163.3 milliseconds 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1364 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 6 sheets defined 50.7% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.601A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.681A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 90 removed outlier: 3.978A pdb=" N LEU A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 90 through 105 Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 122 through 151 Processing helix chain 'A' and resid 193 through 203 Processing helix chain 'A' and resid 219 through 233 Processing helix chain 'A' and resid 251 through 265 Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.820A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.764A pdb=" N SER A 314 " --> pdb=" O THR A 310 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 356 Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 372 through 380 Processing helix chain 'A' and resid 383 through 418 Processing helix chain 'A' and resid 425 through 442 removed outlier: 3.757A pdb=" N ILE A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.922A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 496 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 510 through 526 removed outlier: 3.576A pdb=" N LEU A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 555 removed outlier: 4.014A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 568 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.235A pdb=" N ALA L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.551A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLY H 16 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER H 85 " --> pdb=" O GLY H 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.583A pdb=" N THR H 113 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR H 94 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.583A pdb=" N THR H 113 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR H 94 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 531 through 532 Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 6 removed outlier: 12.089A pdb=" N CYS L 23 " --> pdb=" O THR L 75 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N THR L 75 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 11.155A pdb=" N ALA L 25 " --> pdb=" O SER L 73 " (cutoff:3.500A) removed outlier: 11.094A pdb=" N SER L 73 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.986A pdb=" N SER L 27 " --> pdb=" O SER L 71 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER L 71 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY L 69 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.344A pdb=" N MET L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 885 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: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1712 1.34 - 1.46: 1446 1.46 - 1.58: 2881 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 6099 Sorted by residual: bond pdb=" C4 IZC A1002 " pdb=" C5 IZC A1002 " ideal model delta sigma weight residual 1.482 1.355 0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" C2 IZC A1002 " pdb=" N1 IZC A1002 " ideal model delta sigma weight residual 1.441 1.336 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C2 IZC A1002 " pdb=" N3 IZC A1002 " ideal model delta sigma weight residual 1.437 1.337 0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" C PHE A 67 " pdb=" N PRO A 68 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.09e+00 bond pdb=" CG LEU A 398 " pdb=" CD1 LEU A 398 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.88e+00 ... (remaining 6094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 8111 2.77 - 5.54: 154 5.54 - 8.31: 21 8.31 - 11.07: 3 11.07 - 13.84: 2 Bond angle restraints: 8291 Sorted by residual: angle pdb=" C SER L 51 " pdb=" N THR L 52 " pdb=" CA THR L 52 " ideal model delta sigma weight residual 121.54 131.46 -9.92 1.91e+00 2.74e-01 2.70e+01 angle pdb=" C4 IZC A1002 " pdb=" C6 IZC A1002 " pdb=" C7 IZC A1002 " ideal model delta sigma weight residual 121.54 107.70 13.84 3.00e+00 1.11e-01 2.13e+01 angle pdb=" C TRP A 218 " pdb=" N ASP A 219 " pdb=" CA ASP A 219 " ideal model delta sigma weight residual 121.54 129.57 -8.03 1.91e+00 2.74e-01 1.77e+01 angle pdb=" CB MET A 452 " pdb=" CG MET A 452 " pdb=" SD MET A 452 " ideal model delta sigma weight residual 112.70 124.48 -11.78 3.00e+00 1.11e-01 1.54e+01 angle pdb=" C GLY L 30 " pdb=" N SER L 31 " pdb=" CA SER L 31 " ideal model delta sigma weight residual 121.54 128.56 -7.02 1.91e+00 2.74e-01 1.35e+01 ... (remaining 8286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 3102 16.36 - 32.71: 308 32.71 - 49.07: 69 49.07 - 65.42: 11 65.42 - 81.78: 6 Dihedral angle restraints: 3496 sinusoidal: 1337 harmonic: 2159 Sorted by residual: dihedral pdb=" CB CYS A 162 " pdb=" SG CYS A 162 " pdb=" SG CYS A 171 " pdb=" CB CYS A 171 " ideal model delta sinusoidal sigma weight residual 93.00 174.78 -81.78 1 1.00e+01 1.00e-02 8.23e+01 dihedral pdb=" CA TYR L 95 " pdb=" C TYR L 95 " pdb=" N PRO L 96 " pdb=" CA PRO L 96 " ideal model delta harmonic sigma weight residual 180.00 154.71 25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA SER L 31 " pdb=" C SER L 31 " pdb=" N SER L 32 " pdb=" CA SER L 32 " ideal model delta harmonic sigma weight residual 180.00 157.50 22.50 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 3493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 707 0.057 - 0.113: 157 0.113 - 0.170: 36 0.170 - 0.226: 6 0.226 - 0.283: 2 Chirality restraints: 908 Sorted by residual: chirality pdb=" CB VAL A 140 " pdb=" CA VAL A 140 " pdb=" CG1 VAL A 140 " pdb=" CG2 VAL A 140 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE H 70 " pdb=" CA ILE H 70 " pdb=" CG1 ILE H 70 " pdb=" CG2 ILE H 70 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CG LEU A 312 " pdb=" CB LEU A 312 " pdb=" CD1 LEU A 312 " pdb=" CD2 LEU A 312 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 905 not shown) Planarity restraints: 1022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 92 " -0.051 5.00e-02 4.00e+02 7.63e-02 9.31e+00 pdb=" N PRO A 93 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 479 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.09e+00 pdb=" C ILE A 479 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE A 479 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA A 480 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 219 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.80e+00 pdb=" C ASP A 219 " 0.048 2.00e-02 2.50e+03 pdb=" O ASP A 219 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU A 220 " -0.016 2.00e-02 2.50e+03 ... (remaining 1019 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 858 2.76 - 3.29: 5637 3.29 - 3.83: 10607 3.83 - 4.36: 12692 4.36 - 4.90: 21815 Nonbonded interactions: 51609 Sorted by model distance: nonbonded pdb=" OE1 GLN L 6 " pdb=" OG1 THR L 103 " model vdw 2.221 3.040 nonbonded pdb=" O ASP A 459 " pdb=" OG SER A 464 " model vdw 2.238 3.040 nonbonded pdb=" OH TYR A 69 " pdb=" OD2 ASP A 459 " model vdw 2.242 3.040 nonbonded pdb=" OD1 ASP L 83 " pdb=" OH TYR L 87 " model vdw 2.257 3.040 nonbonded pdb=" O ILE A 496 " pdb=" OH TYR L 33 " model vdw 2.276 3.040 ... (remaining 51604 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.690 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.470 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 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 : 0.006 0.127 6102 Z= 0.282 Angle : 0.933 13.843 8297 Z= 0.494 Chirality : 0.054 0.283 908 Planarity : 0.008 0.076 1022 Dihedral : 13.928 80.655 2123 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -2.31 (0.28), residues: 745 helix: -1.11 (0.24), residues: 346 sheet: -1.63 (0.52), residues: 106 loop : -1.83 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 499 TYR 0.029 0.002 TYR A 137 PHE 0.031 0.003 PHE A 338 TRP 0.017 0.002 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.28 ( 6099) covalent geometry : angle 0.93227 / 0.49 ( 8291) SS BOND : bond 0.00141 / 0.07 ( 3) SS BOND : angle 1.68508 / 0.94 ( 6) hydrogen bonds : bond 0.16884 / 11.45 ( 305) hydrogen bonds : angle 7.90694 / 5.57 ( 885) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 289 GLN cc_start: 0.7851 (pt0) cc_final: 0.7545 (pt0) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0655 time to fit residues: 5.5459 Evaluate side-chains 56 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.242750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.220363 restraints weight = 6134.950| |-----------------------------------------------------------------------------| r_work (start): 0.4453 rms_B_bonded: 1.49 r_work (final): 0.4453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6102 Z= 0.186 Angle : 0.617 7.262 8297 Z= 0.325 Chirality : 0.042 0.159 908 Planarity : 0.006 0.069 1022 Dihedral : 5.547 48.843 833 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.47 % Allowed : 7.22 % Favored : 92.31 % 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: -1.40 (0.30), residues: 745 helix: -0.17 (0.26), residues: 358 sheet: -1.69 (0.53), residues: 101 loop : -1.47 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 62 TYR 0.021 0.001 TYR A 137 PHE 0.015 0.002 PHE A 338 TRP 0.020 0.001 TRP A 470 HIS 0.002 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 ( 6099) covalent geometry : angle 0.61676 / 0.33 ( 8291) SS BOND : bond 0.00157 / 0.08 ( 3) SS BOND : angle 0.78790 / 0.42 ( 6) hydrogen bonds : bond 0.04864 / 3.45 ( 305) hydrogen bonds : angle 5.79606 / 3.95 ( 885) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.167 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 54 average time/residue: 0.0543 time to fit residues: 4.1554 Evaluate side-chains 53 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 25 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 GLN ** 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 = 0.4587 r_free = 0.4587 target = 0.237057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.213471 restraints weight = 6096.259| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 1.54 r_work: 0.4030 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6102 Z= 0.234 Angle : 0.649 12.116 8297 Z= 0.336 Chirality : 0.043 0.155 908 Planarity : 0.006 0.066 1022 Dihedral : 5.498 51.025 833 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.11 % Favored : 92.75 % Rotamer: Outliers : 1.41 % Allowed : 9.73 % Favored : 88.85 % 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: -1.16 (0.30), residues: 745 helix: 0.05 (0.27), residues: 357 sheet: -1.75 (0.53), residues: 98 loop : -1.31 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 66 TYR 0.021 0.002 TYR A 137 PHE 0.017 0.002 PHE A 392 TRP 0.019 0.002 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.23 ( 6099) covalent geometry : angle 0.64947 / 0.34 ( 8291) SS BOND : bond 0.00169 / 0.09 ( 3) SS BOND : angle 0.64459 / 0.33 ( 6) hydrogen bonds : bond 0.04944 / 3.50 ( 305) hydrogen bonds : angle 5.75526 / 3.91 ( 885) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.154 Fit side-chains REVERT: A 304 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7087 (tp) outliers start: 9 outliers final: 5 residues processed: 64 average time/residue: 0.0800 time to fit residues: 6.6956 Evaluate side-chains 63 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 0.0020 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 = 0.4609 r_free = 0.4609 target = 0.238727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.218037 restraints weight = 6076.906| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 1.33 r_work: 0.4176 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6102 Z= 0.194 Angle : 0.608 11.946 8297 Z= 0.314 Chirality : 0.041 0.156 908 Planarity : 0.005 0.064 1022 Dihedral : 5.310 53.724 833 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.04 % Favored : 93.83 % Rotamer: Outliers : 1.57 % Allowed : 11.77 % Favored : 86.66 % 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: -1.02 (0.30), residues: 745 helix: 0.22 (0.27), residues: 359 sheet: -1.74 (0.50), residues: 104 loop : -1.28 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.022 0.001 TYR A 137 PHE 0.016 0.002 PHE A 392 TRP 0.019 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 ( 6099) covalent geometry : angle 0.60806 / 0.31 ( 8291) SS BOND : bond 0.00189 / 0.10 ( 3) SS BOND : angle 0.60775 / 0.30 ( 6) hydrogen bonds : bond 0.04572 / 3.25 ( 305) hydrogen bonds : angle 5.57082 / 3.78 ( 885) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.211 Fit side-chains REVERT: A 304 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.6892 (tp) outliers start: 10 outliers final: 7 residues processed: 67 average time/residue: 0.0715 time to fit residues: 6.3760 Evaluate side-chains 66 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 33 optimal weight: 0.0870 chunk 63 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 0.0770 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- 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 = 0.4634 r_free = 0.4634 target = 0.241909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.221017 restraints weight = 6197.956| |-----------------------------------------------------------------------------| r_work (start): 0.4451 rms_B_bonded: 1.38 r_work: 0.4188 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6102 Z= 0.156 Angle : 0.580 13.049 8297 Z= 0.297 Chirality : 0.040 0.160 908 Planarity : 0.005 0.059 1022 Dihedral : 5.162 58.866 833 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.04 % Favored : 93.83 % Rotamer: Outliers : 1.57 % Allowed : 13.34 % Favored : 85.09 % 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: -0.81 (0.31), residues: 745 helix: 0.46 (0.27), residues: 359 sheet: -1.73 (0.50), residues: 104 loop : -1.25 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.023 0.001 TYR A 137 PHE 0.014 0.001 PHE A 392 TRP 0.018 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 6099) covalent geometry : angle 0.57955 / 0.30 ( 8291) SS BOND : bond 0.00168 / 0.08 ( 3) SS BOND : angle 0.56195 / 0.28 ( 6) hydrogen bonds : bond 0.04240 / 3.03 ( 305) hydrogen bonds : angle 5.36034 / 3.64 ( 885) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.157 Fit side-chains REVERT: A 304 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.6898 (tp) outliers start: 10 outliers final: 7 residues processed: 65 average time/residue: 0.0870 time to fit residues: 7.5256 Evaluate side-chains 60 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 14 optimal weight: 0.0670 chunk 50 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.240711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.220340 restraints weight = 6130.518| |-----------------------------------------------------------------------------| r_work (start): 0.4435 rms_B_bonded: 1.33 r_work: 0.4229 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4084 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6102 Z= 0.165 Angle : 0.587 13.876 8297 Z= 0.299 Chirality : 0.041 0.224 908 Planarity : 0.005 0.059 1022 Dihedral : 5.049 56.982 833 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.58 % Favored : 93.29 % Rotamer: Outliers : 1.73 % Allowed : 13.66 % Favored : 84.62 % 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: -0.83 (0.31), residues: 745 helix: 0.50 (0.27), residues: 362 sheet: -1.93 (0.48), residues: 110 loop : -1.24 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.022 0.001 TYR A 137 PHE 0.015 0.001 PHE A 392 TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 6099) covalent geometry : angle 0.58659 / 0.30 ( 8291) SS BOND : bond 0.00163 / 0.08 ( 3) SS BOND : angle 0.53623 / 0.27 ( 6) hydrogen bonds : bond 0.04277 / 3.06 ( 305) hydrogen bonds : angle 5.32059 / 3.61 ( 885) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.227 Fit side-chains REVERT: A 304 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.6920 (tp) outliers start: 11 outliers final: 7 residues processed: 63 average time/residue: 0.0827 time to fit residues: 6.8901 Evaluate side-chains 61 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 65 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.236682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.213532 restraints weight = 6185.349| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 1.52 r_work: 0.4043 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6102 Z= 0.211 Angle : 0.623 12.929 8297 Z= 0.319 Chirality : 0.042 0.204 908 Planarity : 0.005 0.060 1022 Dihedral : 5.088 51.980 833 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.44 % Favored : 93.42 % Rotamer: Outliers : 1.88 % Allowed : 14.44 % Favored : 83.67 % 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: -0.87 (0.31), residues: 745 helix: 0.40 (0.27), residues: 358 sheet: -1.85 (0.49), residues: 104 loop : -1.20 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.022 0.002 TYR A 137 PHE 0.016 0.002 PHE A 392 TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 ( 6099) covalent geometry : angle 0.62329 / 0.32 ( 8291) SS BOND : bond 0.00176 / 0.09 ( 3) SS BOND : angle 0.52101 / 0.26 ( 6) hydrogen bonds : bond 0.04564 / 3.26 ( 305) hydrogen bonds : angle 5.43895 / 3.70 ( 885) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.205 Fit side-chains REVERT: A 304 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7077 (tp) outliers start: 12 outliers final: 9 residues processed: 64 average time/residue: 0.0905 time to fit residues: 7.6767 Evaluate side-chains 64 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4416 r_free = 0.4416 target = 0.218791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.194529 restraints weight = 6303.921| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 1.62 r_work: 0.3933 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6102 Z= 0.194 Angle : 0.609 12.638 8297 Z= 0.312 Chirality : 0.042 0.190 908 Planarity : 0.005 0.060 1022 Dihedral : 4.999 48.905 833 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.41 % Allowed : 16.01 % Favored : 82.57 % 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: -0.88 (0.31), residues: 745 helix: 0.44 (0.27), residues: 358 sheet: -1.93 (0.51), residues: 98 loop : -1.27 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.022 0.001 TYR A 137 PHE 0.016 0.002 PHE A 392 TRP 0.018 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 ( 6099) covalent geometry : angle 0.60888 / 0.31 ( 8291) SS BOND : bond 0.00169 / 0.08 ( 3) SS BOND : angle 0.56169 / 0.28 ( 6) hydrogen bonds : bond 0.04435 / 3.17 ( 305) hydrogen bonds : angle 5.40313 / 3.67 ( 885) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.225 Fit side-chains REVERT: A 304 ILE cc_start: 0.7396 (OUTLIER) cc_final: 0.6918 (tp) outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.0955 time to fit residues: 7.7124 Evaluate side-chains 65 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 64 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.0980 chunk 43 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.217488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.193220 restraints weight = 6354.546| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.61 r_work: 0.3936 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6102 Z= 0.207 Angle : 0.624 12.323 8297 Z= 0.319 Chirality : 0.042 0.186 908 Planarity : 0.005 0.060 1022 Dihedral : 4.962 42.470 833 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.58 % Favored : 93.29 % Rotamer: Outliers : 1.57 % Allowed : 16.80 % Favored : 81.63 % 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: -0.95 (0.30), residues: 745 helix: 0.38 (0.27), residues: 360 sheet: -2.00 (0.50), residues: 98 loop : -1.31 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.022 0.002 TYR A 137 PHE 0.016 0.002 PHE A 392 TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 ( 6099) covalent geometry : angle 0.62359 / 0.32 ( 8291) SS BOND : bond 0.00174 / 0.09 ( 3) SS BOND : angle 0.55183 / 0.28 ( 6) hydrogen bonds : bond 0.04529 / 3.24 ( 305) hydrogen bonds : angle 5.44692 / 3.70 ( 885) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.218 Fit side-chains REVERT: A 256 MET cc_start: 0.7874 (tpt) cc_final: 0.7364 (tpt) REVERT: A 304 ILE cc_start: 0.7385 (OUTLIER) cc_final: 0.6898 (tp) outliers start: 10 outliers final: 9 residues processed: 61 average time/residue: 0.0968 time to fit residues: 7.7172 Evaluate side-chains 63 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 45 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 0.0770 chunk 12 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 29 optimal weight: 0.0980 chunk 5 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 overall best weight: 0.3338 ------------------------------------------------------------------------------- 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 = 0.4642 r_free = 0.4642 target = 0.243158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.221064 restraints weight = 6153.144| |-----------------------------------------------------------------------------| r_work (start): 0.4456 rms_B_bonded: 1.52 r_work: 0.4123 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6102 Z= 0.136 Angle : 0.568 12.319 8297 Z= 0.291 Chirality : 0.040 0.161 908 Planarity : 0.005 0.057 1022 Dihedral : 4.691 39.038 833 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.73 % Allowed : 16.95 % Favored : 81.32 % 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: -0.67 (0.31), residues: 745 helix: 0.69 (0.27), residues: 358 sheet: -1.88 (0.51), residues: 98 loop : -1.28 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 499 TYR 0.024 0.001 TYR A 137 PHE 0.013 0.001 PHE A 392 TRP 0.018 0.001 TRP A 470 HIS 0.003 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 6099) covalent geometry : angle 0.56789 / 0.29 ( 8291) SS BOND : bond 0.00186 / 0.09 ( 3) SS BOND : angle 0.56106 / 0.27 ( 6) hydrogen bonds : bond 0.04024 / 2.88 ( 305) hydrogen bonds : angle 5.18693 / 3.52 ( 885) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.206 Fit side-chains REVERT: A 304 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6709 (tp) outliers start: 11 outliers final: 9 residues processed: 59 average time/residue: 0.0703 time to fit residues: 5.7236 Evaluate side-chains 59 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 50 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4439 r_free = 0.4439 target = 0.220530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.196700 restraints weight = 6271.214| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 1.62 r_work: 0.3907 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6102 Z= 0.181 Angle : 0.607 12.171 8297 Z= 0.309 Chirality : 0.041 0.164 908 Planarity : 0.005 0.058 1022 Dihedral : 4.732 34.247 833 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.57 % Allowed : 17.27 % Favored : 81.16 % 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 (0.31), residues: 745 helix: 0.56 (0.27), residues: 359 sheet: -1.93 (0.50), residues: 98 loop : -1.23 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 493 TYR 0.022 0.001 TYR A 137 PHE 0.015 0.001 PHE A 392 TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 ( 6099) covalent geometry : angle 0.60690 / 0.31 ( 8291) SS BOND : bond 0.00157 / 0.08 ( 3) SS BOND : angle 0.54652 / 0.28 ( 6) hydrogen bonds : bond 0.04334 / 3.10 ( 305) hydrogen bonds : angle 5.31576 / 3.61 ( 885) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1314.91 seconds wall clock time: 23 minutes 23.54 seconds (1403.54 seconds total)