Starting phenix.real_space_refine on Thu Jul 2 02:34:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n6b_24206/07_2026/7n6b_24206.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n6b_24206/07_2026/7n6b_24206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n6b_24206/07_2026/7n6b_24206.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n6b_24206/07_2026/7n6b_24206.map" model { file = "/net/cci-nas-00/data/ceres_data/7n6b_24206/07_2026/7n6b_24206.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n6b_24206/07_2026/7n6b_24206.cif" } resolution = 2.66 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 ------------------------------------------------------------------------------- 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= 0.409 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 3871 2.51 5 N 963 2.21 5 O 1080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s 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: 5942 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5803 Classifications: {'peptide': 757} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 38, 'TRANS': 718} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 139 Unusual residues: {'0HJ': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Time building chain proxies: 1.32, per 1000 atoms: 0.22 Number of scatterers: 5942 At special positions: 0 Unit cell: (108.07, 89.88, 83.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1080 8.00 N 963 7.00 C 3871 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 368.7 milliseconds 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1390 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 3 sheets defined 72.8% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 removed outlier: 3.636A pdb=" N TRP A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR A 10 " --> pdb=" O GLY A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 32 removed outlier: 3.558A pdb=" N ILE A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY A 18 " --> pdb=" O TYR A 14 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N CYS A 24 " --> pdb=" O MET A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 removed outlier: 4.075A pdb=" N VAL A 38 " --> pdb=" O GLY A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 62 Processing helix chain 'A' and resid 83 through 101 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 143 through 159 Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 171 through 192 removed outlier: 3.603A pdb=" N GLU A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 206 removed outlier: 3.674A pdb=" N LEU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 233 Proline residue: A 214 - end of helix Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 249 through 272 Processing helix chain 'A' and resid 274 through 302 removed outlier: 3.507A pdb=" N THR A 285 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG A 288 " --> pdb=" O MET A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 309 through 342 removed outlier: 3.612A pdb=" N ILE A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 350 through 356 removed outlier: 4.025A pdb=" N LEU A 354 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 350 through 356' Processing helix chain 'A' and resid 365 through 377 removed outlier: 3.757A pdb=" N TRP A 371 " --> pdb=" O ARG A 367 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 removed outlier: 3.539A pdb=" N GLU A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 400 removed outlier: 6.150A pdb=" N VAL A 394 " --> pdb=" O TRP A 390 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 removed outlier: 4.483A pdb=" N VAL A 411 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.599A pdb=" N GLN A 421 " --> pdb=" O PRO A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 432 Processing helix chain 'A' and resid 436 through 449 Processing helix chain 'A' and resid 470 through 483 removed outlier: 3.590A pdb=" N ILE A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 548 through 563 Processing helix chain 'A' and resid 563 through 584 Processing helix chain 'A' and resid 586 through 612 removed outlier: 3.784A pdb=" N ILE A 590 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 661 removed outlier: 3.605A pdb=" N LEU A 634 " --> pdb=" O PRO A 630 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 692 removed outlier: 4.941A pdb=" N ARG A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 718 Processing helix chain 'A' and resid 723 through 732 Processing helix chain 'A' and resid 733 through 737 removed outlier: 3.530A pdb=" N TRP A 736 " --> pdb=" O ASP A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 748 removed outlier: 3.660A pdb=" N VAL A 745 " --> pdb=" O TRP A 741 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA2, first strand: chain 'A' and resid 424 through 425 Processing sheet with id=AA3, first strand: chain 'A' and resid 499 through 500 391 hydrogen bonds defined for protein. 1110 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: 0.90 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 961 1.30 - 1.43: 1413 1.43 - 1.56: 3605 1.56 - 1.68: 30 1.68 - 1.81: 54 Bond restraints: 6063 Sorted by residual: bond pdb=" C04 0HJ A1101 " pdb=" O05 0HJ A1101 " ideal model delta sigma weight residual 1.394 1.541 -0.147 2.00e-02 2.50e+03 5.40e+01 bond pdb=" C04 0HJ A1102 " pdb=" O05 0HJ A1102 " ideal model delta sigma weight residual 1.394 1.536 -0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" C12 0HJ A1101 " pdb=" O13 0HJ A1101 " ideal model delta sigma weight residual 1.417 1.540 -0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" C12 0HJ A1102 " pdb=" O13 0HJ A1102 " ideal model delta sigma weight residual 1.417 1.537 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" C04 0HJ A1102 " pdb=" O07 0HJ A1102 " ideal model delta sigma weight residual 1.398 1.303 0.095 2.00e-02 2.50e+03 2.28e+01 ... (remaining 6058 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 7970 2.23 - 4.46: 193 4.46 - 6.69: 59 6.69 - 8.92: 4 8.92 - 11.15: 2 Bond angle restraints: 8228 Sorted by residual: angle pdb=" N ILE A 408 " pdb=" CA ILE A 408 " pdb=" C ILE A 408 " ideal model delta sigma weight residual 111.90 108.46 3.44 8.10e-01 1.52e+00 1.81e+01 angle pdb=" N PHE A 722 " pdb=" CA PHE A 722 " pdb=" C PHE A 722 " ideal model delta sigma weight residual 110.61 115.46 -4.85 1.25e+00 6.40e-01 1.50e+01 angle pdb=" C26 0HJ A1101 " pdb=" C24 0HJ A1101 " pdb=" O23 0HJ A1101 " ideal model delta sigma weight residual 112.34 123.49 -11.15 3.00e+00 1.11e-01 1.38e+01 angle pdb=" C THR A 133 " pdb=" N PHE A 134 " pdb=" CA PHE A 134 " ideal model delta sigma weight residual 122.21 116.40 5.81 1.62e+00 3.81e-01 1.29e+01 angle pdb=" C09 0HJ A1101 " pdb=" C08 0HJ A1101 " pdb=" O07 0HJ A1101 " ideal model delta sigma weight residual 108.12 116.70 -8.58 3.00e+00 1.11e-01 8.17e+00 ... (remaining 8223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.02: 3560 31.02 - 62.05: 132 62.05 - 93.07: 27 93.07 - 124.10: 18 124.10 - 155.12: 11 Dihedral angle restraints: 3748 sinusoidal: 1590 harmonic: 2158 Sorted by residual: dihedral pdb=" CA PHE A 722 " pdb=" C PHE A 722 " pdb=" N LEU A 723 " pdb=" CA LEU A 723 " ideal model delta harmonic sigma weight residual 180.00 155.39 24.61 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" C60 0HJ A1101 " pdb=" C61 0HJ A1101 " pdb=" C67 0HJ A1101 " pdb=" C71 0HJ A1101 " ideal model delta sinusoidal sigma weight residual 278.07 122.95 155.12 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" C60 0HJ A1101 " pdb=" C61 0HJ A1101 " pdb=" C67 0HJ A1101 " pdb=" C68 0HJ A1101 " ideal model delta sinusoidal sigma weight residual 207.29 55.22 152.07 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 3745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 865 0.072 - 0.143: 107 0.143 - 0.215: 8 0.215 - 0.287: 2 0.287 - 0.358: 5 Chirality restraints: 987 Sorted by residual: chirality pdb=" C68 0HJ A1102 " pdb=" C67 0HJ A1102 " pdb=" C69 0HJ A1102 " pdb=" C71 0HJ A1102 " both_signs ideal model delta sigma weight residual True 2.38 2.74 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" C68 0HJ A1101 " pdb=" C67 0HJ A1101 " pdb=" C69 0HJ A1101 " pdb=" C71 0HJ A1101 " both_signs ideal model delta sigma weight residual True 2.38 2.73 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C67 0HJ A1102 " pdb=" C61 0HJ A1102 " pdb=" C68 0HJ A1102 " pdb=" C71 0HJ A1102 " both_signs ideal model delta sigma weight residual True 2.39 -2.73 -0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 984 not shown) Planarity restraints: 1018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 75 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO A 76 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 283 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C VAL A 283 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL A 283 " -0.014 2.00e-02 2.50e+03 pdb=" N MET A 284 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 391 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C GLY A 391 " -0.034 2.00e-02 2.50e+03 pdb=" O GLY A 391 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A 392 " 0.012 2.00e-02 2.50e+03 ... (remaining 1015 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 125 2.70 - 3.25: 6122 3.25 - 3.80: 9889 3.80 - 4.35: 13039 4.35 - 4.90: 21073 Nonbonded interactions: 50248 Sorted by model distance: nonbonded pdb=" O MET A 610 " pdb=" OH TYR A 622 " model vdw 2.147 3.040 nonbonded pdb=" O LEU A 713 " pdb=" OG1 THR A 717 " model vdw 2.156 3.040 nonbonded pdb=" OD1 ASP A 185 " pdb=" NH2 ARG A 188 " model vdw 2.220 3.120 nonbonded pdb=" O TRP A 108 " pdb=" NZ LYS A 113 " model vdw 2.249 3.120 nonbonded pdb=" O SER A 485 " pdb=" NZ LYS A 529 " model vdw 2.311 3.120 ... (remaining 50243 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: 0.070 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.700 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:5.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.147 6063 Z= 0.408 Angle : 0.875 11.153 8228 Z= 0.415 Chirality : 0.055 0.358 987 Planarity : 0.005 0.055 1018 Dihedral : 20.830 155.120 2358 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: 0.66 (0.31), residues: 753 helix: 0.89 (0.24), residues: 483 sheet: 0.32 (0.74), residues: 47 loop : -0.31 (0.43), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 720 TYR 0.015 0.002 TYR A 646 PHE 0.024 0.002 PHE A 134 TRP 0.008 0.002 TRP A 5 HIS 0.005 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00841 / 0.41 ( 6063) covalent geometry : angle 0.87486 / 0.41 ( 8228) hydrogen bonds : bond 0.14253 / 9.26 ( 391) hydrogen bonds : angle 5.49036 / 4.05 ( 1110) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.174 Fit side-chains REVERT: A 40 GLN cc_start: 0.7366 (tm-30) cc_final: 0.7019 (tm-30) REVERT: A 604 MET cc_start: 0.7627 (mmm) cc_final: 0.7155 (mmm) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.4530 time to fit residues: 75.1692 Evaluate side-chains 133 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN A 444 GLN A 504 ASN A 518 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.189722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.171250 restraints weight = 7346.514| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.51 r_work: 0.3733 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6063 Z= 0.241 Angle : 0.770 11.954 8228 Z= 0.373 Chirality : 0.049 0.283 987 Planarity : 0.006 0.036 1018 Dihedral : 21.502 143.462 1011 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.90 % Allowed : 11.45 % Favored : 85.65 % 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: 0.70 (0.31), residues: 753 helix: 0.89 (0.24), residues: 490 sheet: 0.12 (0.73), residues: 47 loop : -0.22 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 280 TYR 0.017 0.002 TYR A 646 PHE 0.030 0.003 PHE A 722 TRP 0.013 0.002 TRP A 86 HIS 0.006 0.002 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.24 ( 6063) covalent geometry : angle 0.76954 / 0.37 ( 8228) hydrogen bonds : bond 0.04587 / 2.98 ( 391) hydrogen bonds : angle 4.61578 / 3.37 ( 1110) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 40 GLN cc_start: 0.7628 (tm-30) cc_final: 0.7257 (tm-30) REVERT: A 366 ARG cc_start: 0.5085 (OUTLIER) cc_final: 0.4271 (tmm160) REVERT: A 395 ASN cc_start: 0.7934 (m-40) cc_final: 0.7616 (m110) REVERT: A 455 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7996 (pt0) REVERT: A 604 MET cc_start: 0.8258 (mmm) cc_final: 0.7752 (mmm) REVERT: A 659 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7522 (mm-30) REVERT: A 677 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7931 (ttp80) REVERT: A 740 ARG cc_start: 0.4965 (OUTLIER) cc_final: 0.4300 (tmt170) outliers start: 18 outliers final: 4 residues processed: 155 average time/residue: 0.4713 time to fit residues: 77.0467 Evaluate side-chains 142 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 740 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 39 optimal weight: 0.0040 chunk 22 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN A 504 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.193253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.174740 restraints weight = 7276.674| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.56 r_work: 0.3773 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6063 Z= 0.138 Angle : 0.668 14.471 8228 Z= 0.311 Chirality : 0.045 0.305 987 Planarity : 0.005 0.035 1018 Dihedral : 18.216 145.979 1011 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.94 % Allowed : 14.68 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.32), residues: 753 helix: 1.14 (0.24), residues: 490 sheet: 0.09 (0.74), residues: 47 loop : 0.02 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 280 TYR 0.012 0.002 TYR A 10 PHE 0.021 0.002 PHE A 580 TRP 0.009 0.001 TRP A 741 HIS 0.003 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 6063) covalent geometry : angle 0.66819 / 0.31 ( 8228) hydrogen bonds : bond 0.03644 / 2.36 ( 391) hydrogen bonds : angle 4.33500 / 3.18 ( 1110) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.224 Fit side-chains REVERT: A 40 GLN cc_start: 0.7571 (tm-30) cc_final: 0.7194 (tm-30) REVERT: A 395 ASN cc_start: 0.7764 (m-40) cc_final: 0.7451 (m110) REVERT: A 455 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7951 (pt0) REVERT: A 604 MET cc_start: 0.8252 (mmm) cc_final: 0.7817 (mmm) REVERT: A 613 ASP cc_start: 0.7715 (t70) cc_final: 0.7426 (t70) REVERT: A 628 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7575 (ttp) REVERT: A 659 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7406 (mm-30) outliers start: 12 outliers final: 3 residues processed: 155 average time/residue: 0.4337 time to fit residues: 71.0097 Evaluate side-chains 143 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 722 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN A 421 GLN A 504 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.189861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.170768 restraints weight = 7316.722| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.54 r_work: 0.3730 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6063 Z= 0.235 Angle : 0.726 7.585 8228 Z= 0.354 Chirality : 0.049 0.317 987 Planarity : 0.005 0.036 1018 Dihedral : 17.340 149.123 1011 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.03 % Allowed : 15.97 % Favored : 80.00 % 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: 0.86 (0.31), residues: 753 helix: 1.09 (0.24), residues: 480 sheet: -0.09 (0.73), residues: 47 loop : -0.22 (0.45), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 367 TYR 0.015 0.002 TYR A 646 PHE 0.027 0.002 PHE A 580 TRP 0.011 0.002 TRP A 86 HIS 0.005 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.23 ( 6063) covalent geometry : angle 0.72637 / 0.35 ( 8228) hydrogen bonds : bond 0.04232 / 2.74 ( 391) hydrogen bonds : angle 4.51278 / 3.31 ( 1110) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 40 GLN cc_start: 0.7652 (tm-30) cc_final: 0.7232 (tm-30) REVERT: A 366 ARG cc_start: 0.4753 (OUTLIER) cc_final: 0.3909 (tmm160) REVERT: A 395 ASN cc_start: 0.7988 (m-40) cc_final: 0.7655 (m110) REVERT: A 455 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7941 (pt0) REVERT: A 578 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8493 (mp) REVERT: A 595 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8307 (mtt) REVERT: A 604 MET cc_start: 0.8283 (mmm) cc_final: 0.7805 (mmm) REVERT: A 628 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7586 (ttp) REVERT: A 659 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7352 (mm-30) REVERT: A 677 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8149 (ttm-80) REVERT: A 740 ARG cc_start: 0.6139 (mtm-85) cc_final: 0.5578 (tmt170) outliers start: 25 outliers final: 10 residues processed: 157 average time/residue: 0.4572 time to fit residues: 75.7988 Evaluate side-chains 154 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 735 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 504 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.192832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.174615 restraints weight = 7424.999| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.48 r_work: 0.3772 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6063 Z= 0.128 Angle : 0.634 7.399 8228 Z= 0.300 Chirality : 0.045 0.298 987 Planarity : 0.005 0.037 1018 Dihedral : 15.947 150.166 1011 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.03 % Allowed : 16.94 % Favored : 79.03 % 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: 1.13 (0.32), residues: 753 helix: 1.25 (0.24), residues: 483 sheet: -0.11 (0.75), residues: 47 loop : 0.03 (0.45), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 280 TYR 0.011 0.002 TYR A 10 PHE 0.021 0.002 PHE A 580 TRP 0.010 0.001 TRP A 741 HIS 0.003 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 6063) covalent geometry : angle 0.63437 / 0.30 ( 8228) hydrogen bonds : bond 0.03454 / 2.22 ( 391) hydrogen bonds : angle 4.30737 / 3.16 ( 1110) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.135 Fit side-chains REVERT: A 40 GLN cc_start: 0.7707 (tm-30) cc_final: 0.7261 (tm-30) REVERT: A 188 ARG cc_start: 0.7532 (ttm-80) cc_final: 0.7249 (ttp-110) REVERT: A 268 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: A 366 ARG cc_start: 0.4762 (OUTLIER) cc_final: 0.3985 (tmm160) REVERT: A 395 ASN cc_start: 0.7781 (m-40) cc_final: 0.7480 (m110) REVERT: A 444 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7466 (tp40) REVERT: A 455 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7888 (pt0) REVERT: A 595 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8320 (mtt) REVERT: A 659 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7334 (mm-30) REVERT: A 677 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8090 (ttm-80) REVERT: A 740 ARG cc_start: 0.6035 (mtm-85) cc_final: 0.5579 (tmt170) outliers start: 25 outliers final: 6 residues processed: 160 average time/residue: 0.4533 time to fit residues: 76.4584 Evaluate side-chains 152 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 735 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.193707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.175334 restraints weight = 7361.230| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.51 r_work: 0.3783 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6063 Z= 0.122 Angle : 0.636 7.823 8228 Z= 0.299 Chirality : 0.044 0.315 987 Planarity : 0.005 0.040 1018 Dihedral : 14.697 148.789 1011 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.55 % Allowed : 18.23 % Favored : 78.23 % 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: 1.28 (0.31), residues: 753 helix: 1.35 (0.24), residues: 484 sheet: -0.09 (0.76), residues: 47 loop : 0.13 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 280 TYR 0.012 0.002 TYR A 10 PHE 0.020 0.001 PHE A 580 TRP 0.011 0.001 TRP A 741 HIS 0.003 0.001 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 6063) covalent geometry : angle 0.63631 / 0.30 ( 8228) hydrogen bonds : bond 0.03347 / 2.15 ( 391) hydrogen bonds : angle 4.23737 / 3.11 ( 1110) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.138 Fit side-chains REVERT: A 20 MET cc_start: 0.6037 (OUTLIER) cc_final: 0.5461 (ttm) REVERT: A 40 GLN cc_start: 0.7702 (tm-30) cc_final: 0.7252 (tm-30) REVERT: A 188 ARG cc_start: 0.7537 (ttm-80) cc_final: 0.7244 (ttp-110) REVERT: A 268 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: A 366 ARG cc_start: 0.4697 (OUTLIER) cc_final: 0.4048 (tmm160) REVERT: A 395 ASN cc_start: 0.7740 (m-40) cc_final: 0.7442 (m110) REVERT: A 444 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7710 (tp40) REVERT: A 455 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7857 (pt0) REVERT: A 595 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8341 (mtt) REVERT: A 659 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7251 (mm-30) REVERT: A 677 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8062 (ttm-80) REVERT: A 740 ARG cc_start: 0.6109 (mtm-85) cc_final: 0.5614 (tmt170) outliers start: 22 outliers final: 6 residues processed: 157 average time/residue: 0.4259 time to fit residues: 70.6582 Evaluate side-chains 151 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 735 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 70 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 20 optimal weight: 0.0770 chunk 12 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.193909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.175323 restraints weight = 7345.091| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.49 r_work: 0.3781 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6063 Z= 0.137 Angle : 0.646 8.358 8228 Z= 0.305 Chirality : 0.045 0.319 987 Planarity : 0.005 0.042 1018 Dihedral : 13.832 145.047 1011 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.39 % Allowed : 19.35 % Favored : 77.26 % 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: 1.33 (0.32), residues: 753 helix: 1.39 (0.24), residues: 484 sheet: -0.10 (0.75), residues: 47 loop : 0.18 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 280 TYR 0.013 0.002 TYR A 10 PHE 0.024 0.002 PHE A 580 TRP 0.010 0.001 TRP A 741 HIS 0.003 0.001 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 6063) covalent geometry : angle 0.64645 / 0.31 ( 8228) hydrogen bonds : bond 0.03489 / 2.24 ( 391) hydrogen bonds : angle 4.25492 / 3.13 ( 1110) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.221 Fit side-chains REVERT: A 20 MET cc_start: 0.6042 (OUTLIER) cc_final: 0.5468 (ttm) REVERT: A 40 GLN cc_start: 0.7641 (tm-30) cc_final: 0.7191 (tm-30) REVERT: A 188 ARG cc_start: 0.7527 (ttm-80) cc_final: 0.7228 (ttp-110) REVERT: A 268 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: A 366 ARG cc_start: 0.4743 (OUTLIER) cc_final: 0.4170 (tmm160) REVERT: A 395 ASN cc_start: 0.7768 (m-40) cc_final: 0.7464 (m110) REVERT: A 455 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7924 (pt0) REVERT: A 595 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8359 (mtt) REVERT: A 659 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7208 (mm-30) REVERT: A 677 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8058 (ttm-80) REVERT: A 740 ARG cc_start: 0.6048 (mtm-85) cc_final: 0.5576 (tmt170) outliers start: 21 outliers final: 9 residues processed: 153 average time/residue: 0.4685 time to fit residues: 75.5848 Evaluate side-chains 152 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 742 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 57 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 18 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 74 optimal weight: 0.1980 chunk 67 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.194733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.176498 restraints weight = 7280.964| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.45 r_work: 0.3792 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6063 Z= 0.122 Angle : 0.650 15.016 8228 Z= 0.300 Chirality : 0.044 0.259 987 Planarity : 0.005 0.045 1018 Dihedral : 13.272 142.222 1011 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.39 % Allowed : 19.03 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.32), residues: 753 helix: 1.36 (0.24), residues: 490 sheet: -0.03 (0.76), residues: 47 loop : 0.10 (0.46), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 63 TYR 0.012 0.001 TYR A 10 PHE 0.023 0.002 PHE A 580 TRP 0.011 0.001 TRP A 741 HIS 0.003 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 6063) covalent geometry : angle 0.64961 / 0.30 ( 8228) hydrogen bonds : bond 0.03322 / 2.13 ( 391) hydrogen bonds : angle 4.22890 / 3.11 ( 1110) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.220 Fit side-chains REVERT: A 20 MET cc_start: 0.6000 (OUTLIER) cc_final: 0.5446 (ttm) REVERT: A 40 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7237 (tm-30) REVERT: A 188 ARG cc_start: 0.7518 (ttm-80) cc_final: 0.7221 (ttp-110) REVERT: A 268 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: A 366 ARG cc_start: 0.4684 (OUTLIER) cc_final: 0.4010 (tmm160) REVERT: A 395 ASN cc_start: 0.7710 (m-40) cc_final: 0.7409 (m110) REVERT: A 455 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7952 (pt0) REVERT: A 595 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8346 (mtt) REVERT: A 659 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7154 (mm-30) REVERT: A 677 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8034 (ttm-80) REVERT: A 740 ARG cc_start: 0.6075 (mtm-85) cc_final: 0.5650 (tmt170) outliers start: 21 outliers final: 9 residues processed: 152 average time/residue: 0.4414 time to fit residues: 70.9070 Evaluate side-chains 149 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 742 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.192903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.174674 restraints weight = 7327.823| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.44 r_work: 0.3768 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6063 Z= 0.158 Angle : 0.674 12.409 8228 Z= 0.320 Chirality : 0.045 0.206 987 Planarity : 0.005 0.049 1018 Dihedral : 13.120 140.285 1011 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.23 % Allowed : 19.84 % Favored : 76.94 % 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: 1.28 (0.32), residues: 753 helix: 1.36 (0.24), residues: 487 sheet: -0.11 (0.75), residues: 47 loop : 0.08 (0.46), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 63 TYR 0.014 0.002 TYR A 10 PHE 0.029 0.002 PHE A 580 TRP 0.008 0.002 TRP A 741 HIS 0.003 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 6063) covalent geometry : angle 0.67408 / 0.32 ( 8228) hydrogen bonds : bond 0.03635 / 2.34 ( 391) hydrogen bonds : angle 4.30503 / 3.16 ( 1110) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.220 Fit side-chains REVERT: A 20 MET cc_start: 0.6095 (OUTLIER) cc_final: 0.5518 (ttm) REVERT: A 40 GLN cc_start: 0.7716 (tm-30) cc_final: 0.7221 (tm-30) REVERT: A 188 ARG cc_start: 0.7561 (ttm-80) cc_final: 0.7260 (ttp-110) REVERT: A 268 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: A 366 ARG cc_start: 0.4703 (OUTLIER) cc_final: 0.4068 (tmm160) REVERT: A 395 ASN cc_start: 0.7780 (m-40) cc_final: 0.7477 (m110) REVERT: A 455 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7984 (pt0) REVERT: A 595 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8366 (mtt) REVERT: A 659 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7238 (mm-30) REVERT: A 677 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8047 (ttm-80) REVERT: A 740 ARG cc_start: 0.6138 (mtm-85) cc_final: 0.5617 (tmt170) outliers start: 20 outliers final: 9 residues processed: 153 average time/residue: 0.4517 time to fit residues: 72.7643 Evaluate side-chains 152 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 742 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 71 optimal weight: 0.0010 chunk 40 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 HIS A 504 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.197097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.179222 restraints weight = 7406.798| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.44 r_work: 0.3822 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6063 Z= 0.110 Angle : 0.633 11.910 8228 Z= 0.296 Chirality : 0.042 0.190 987 Planarity : 0.005 0.051 1018 Dihedral : 12.632 135.481 1011 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.42 % Allowed : 21.45 % Favored : 76.13 % 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: 1.43 (0.32), residues: 753 helix: 1.42 (0.24), residues: 496 sheet: 0.27 (0.88), residues: 41 loop : 0.16 (0.46), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 280 TYR 0.011 0.001 TYR A 10 PHE 0.021 0.001 PHE A 580 TRP 0.012 0.001 TRP A 741 HIS 0.002 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 6063) covalent geometry : angle 0.63271 / 0.30 ( 8228) hydrogen bonds : bond 0.03135 / 2.00 ( 391) hydrogen bonds : angle 4.19417 / 3.08 ( 1110) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 20 MET cc_start: 0.6000 (OUTLIER) cc_final: 0.5497 (ttm) REVERT: A 40 GLN cc_start: 0.7717 (tm-30) cc_final: 0.7206 (tm-30) REVERT: A 188 ARG cc_start: 0.7453 (ttm-80) cc_final: 0.7146 (ttp-110) REVERT: A 366 ARG cc_start: 0.4453 (OUTLIER) cc_final: 0.3709 (tmm160) REVERT: A 395 ASN cc_start: 0.7694 (m-40) cc_final: 0.7412 (m110) REVERT: A 455 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7901 (pt0) REVERT: A 595 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8347 (mtt) REVERT: A 659 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7203 (mm-30) REVERT: A 677 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7991 (ttm-80) REVERT: A 740 ARG cc_start: 0.6004 (mtm-85) cc_final: 0.5470 (tmt170) outliers start: 15 outliers final: 7 residues processed: 153 average time/residue: 0.4272 time to fit residues: 68.9446 Evaluate side-chains 153 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 677 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.0370 chunk 19 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 overall best weight: 1.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 504 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.196794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.177923 restraints weight = 7332.360| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.57 r_work: 0.3806 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6063 Z= 0.115 Angle : 0.627 10.434 8228 Z= 0.298 Chirality : 0.042 0.184 987 Planarity : 0.005 0.050 1018 Dihedral : 12.410 132.349 1011 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.94 % Allowed : 22.90 % Favored : 75.16 % 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: 1.49 (0.32), residues: 753 helix: 1.48 (0.24), residues: 490 sheet: 0.19 (0.78), residues: 47 loop : 0.21 (0.46), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 280 TYR 0.015 0.001 TYR A 10 PHE 0.033 0.002 PHE A 12 TRP 0.013 0.001 TRP A 741 HIS 0.002 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 6063) covalent geometry : angle 0.62729 / 0.30 ( 8228) hydrogen bonds : bond 0.03188 / 2.06 ( 391) hydrogen bonds : angle 4.16206 / 3.05 ( 1110) =============================================================================== Job complete usr+sys time: 2395.10 seconds wall clock time: 41 minutes 30.79 seconds (2490.79 seconds total)