Starting phenix.real_space_refine on Fri Aug 22 16:57:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cl0_45657/08_2025/9cl0_45657.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cl0_45657/08_2025/9cl0_45657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cl0_45657/08_2025/9cl0_45657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cl0_45657/08_2025/9cl0_45657.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cl0_45657/08_2025/9cl0_45657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cl0_45657/08_2025/9cl0_45657.map" } resolution = 2.3 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= 0.002 sd= 0.084 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 30 5.16 5 C 4218 2.51 5 N 1000 2.21 5 O 1018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6266 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3133 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Restraints were copied for chains: B Time building chain proxies: 2.32, per 1000 atoms: 0.37 Number of scatterers: 6266 At special positions: 0 Unit cell: (125.632, 74.048, 73.216, 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 30 16.00 O 1018 8.00 N 1000 7.00 C 4218 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 384.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1428 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 80.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 231 through 257 Processing helix chain 'A' and resid 265 through 296 removed outlier: 4.244A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 312 through 337 Processing helix chain 'A' and resid 346 through 361 Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 384 through 387 removed outlier: 4.255A pdb=" N HIS A 387 " --> pdb=" O ALA A 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 387' Processing helix chain 'A' and resid 390 through 402 Processing helix chain 'A' and resid 403 through 419 removed outlier: 4.187A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 471 removed outlier: 3.692A pdb=" N ALA A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 472 through 502 removed outlier: 4.103A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 removed outlier: 3.619A pdb=" N PHE A 510 " --> pdb=" O ASP A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 581 removed outlier: 4.327A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 619 Proline residue: A 598 - end of helix removed outlier: 3.806A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 257 Processing helix chain 'B' and resid 265 through 296 removed outlier: 4.244A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 312 through 337 Processing helix chain 'B' and resid 346 through 361 Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 384 through 387 removed outlier: 4.255A pdb=" N HIS B 387 " --> pdb=" O ALA B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 387' Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 403 through 419 removed outlier: 4.187A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 471 removed outlier: 3.692A pdb=" N ALA B 449 " --> pdb=" O TYR B 445 " (cutoff:3.500A) Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 472 through 502 removed outlier: 4.103A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL B 478 " --> pdb=" O PHE B 474 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 removed outlier: 3.619A pdb=" N PHE B 510 " --> pdb=" O ASP B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 581 removed outlier: 4.327A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 619 Proline residue: B 598 - end of helix removed outlier: 3.806A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) 451 hydrogen bonds defined for protein. 1353 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 898 1.31 - 1.44: 2094 1.44 - 1.56: 3436 1.56 - 1.69: 4 1.69 - 1.81: 42 Bond restraints: 6474 Sorted by residual: bond pdb=" CA PHE B 394 " pdb=" C PHE B 394 " ideal model delta sigma weight residual 1.524 1.616 -0.092 1.44e-02 4.82e+03 4.07e+01 bond pdb=" CA PHE A 394 " pdb=" C PHE A 394 " ideal model delta sigma weight residual 1.524 1.616 -0.092 1.44e-02 4.82e+03 4.07e+01 bond pdb=" C ASP A 393 " pdb=" N PHE A 394 " ideal model delta sigma weight residual 1.335 1.387 -0.053 1.27e-02 6.20e+03 1.71e+01 bond pdb=" C ASP B 393 " pdb=" N PHE B 394 " ideal model delta sigma weight residual 1.335 1.387 -0.053 1.27e-02 6.20e+03 1.71e+01 bond pdb=" C PHE B 394 " pdb=" O PHE B 394 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.18e-02 7.18e+03 1.65e+01 ... (remaining 6469 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.57: 8778 7.57 - 15.14: 18 15.14 - 22.71: 4 22.71 - 30.28: 6 30.28 - 37.85: 4 Bond angle restraints: 8810 Sorted by residual: angle pdb=" N PHE A 386 " pdb=" CA PHE A 386 " pdb=" C PHE A 386 " ideal model delta sigma weight residual 112.72 146.86 -34.14 1.14e+00 7.69e-01 8.97e+02 angle pdb=" N PHE B 386 " pdb=" CA PHE B 386 " pdb=" C PHE B 386 " ideal model delta sigma weight residual 112.72 146.86 -34.14 1.14e+00 7.69e-01 8.97e+02 angle pdb=" N LEU A 421 " pdb=" CA LEU A 421 " pdb=" C LEU A 421 " ideal model delta sigma weight residual 112.24 150.09 -37.85 1.28e+00 6.10e-01 8.75e+02 angle pdb=" N LEU B 421 " pdb=" CA LEU B 421 " pdb=" C LEU B 421 " ideal model delta sigma weight residual 112.24 150.09 -37.85 1.28e+00 6.10e-01 8.75e+02 angle pdb=" N HIS A 387 " pdb=" CA HIS A 387 " pdb=" C HIS A 387 " ideal model delta sigma weight residual 109.85 80.56 29.29 1.58e+00 4.01e-01 3.44e+02 ... (remaining 8805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 3090 16.28 - 32.56: 426 32.56 - 48.83: 108 48.83 - 65.11: 18 65.11 - 81.39: 8 Dihedral angle restraints: 3650 sinusoidal: 1434 harmonic: 2216 Sorted by residual: dihedral pdb=" N HIS A 387 " pdb=" C HIS A 387 " pdb=" CA HIS A 387 " pdb=" CB HIS A 387 " ideal model delta harmonic sigma weight residual 122.80 83.83 38.97 0 2.50e+00 1.60e-01 2.43e+02 dihedral pdb=" N HIS B 387 " pdb=" C HIS B 387 " pdb=" CA HIS B 387 " pdb=" CB HIS B 387 " ideal model delta harmonic sigma weight residual 122.80 83.83 38.97 0 2.50e+00 1.60e-01 2.43e+02 dihedral pdb=" N LYS A 422 " pdb=" C LYS A 422 " pdb=" CA LYS A 422 " pdb=" CB LYS A 422 " ideal model delta harmonic sigma weight residual 122.80 153.78 -30.98 0 2.50e+00 1.60e-01 1.54e+02 ... (remaining 3647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.262: 956 0.262 - 0.525: 6 0.525 - 0.787: 0 0.787 - 1.049: 2 1.049 - 1.311: 4 Chirality restraints: 968 Sorted by residual: chirality pdb=" CA LYS A 422 " pdb=" N LYS A 422 " pdb=" C LYS A 422 " pdb=" CB LYS A 422 " both_signs ideal model delta sigma weight residual False 2.51 1.20 1.31 2.00e-01 2.50e+01 4.30e+01 chirality pdb=" CA LYS B 422 " pdb=" N LYS B 422 " pdb=" C LYS B 422 " pdb=" CB LYS B 422 " both_signs ideal model delta sigma weight residual False 2.51 1.20 1.31 2.00e-01 2.50e+01 4.30e+01 chirality pdb=" CA LEU A 421 " pdb=" N LEU A 421 " pdb=" C LEU A 421 " pdb=" CB LEU A 421 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.12 2.00e-01 2.50e+01 3.12e+01 ... (remaining 965 not shown) Planarity restraints: 1070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 263 " -0.625 9.50e-02 1.11e+02 2.80e-01 4.80e+01 pdb=" NE ARG B 263 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG B 263 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 263 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 263 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 263 " 0.625 9.50e-02 1.11e+02 2.80e-01 4.80e+01 pdb=" NE ARG A 263 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG A 263 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 263 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 263 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 468 " 0.611 9.50e-02 1.11e+02 2.74e-01 4.61e+01 pdb=" NE ARG B 468 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG B 468 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG B 468 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 468 " 0.023 2.00e-02 2.50e+03 ... (remaining 1067 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 48 2.59 - 3.17: 5328 3.17 - 3.75: 10464 3.75 - 4.32: 13991 4.32 - 4.90: 22470 Nonbonded interactions: 52301 Sorted by model distance: nonbonded pdb=" N HIS A 387 " pdb=" O HIS A 387 " model vdw 2.015 2.496 nonbonded pdb=" N HIS B 387 " pdb=" O HIS B 387 " model vdw 2.015 2.496 nonbonded pdb=" O THR A 261 " pdb=" OD1 ASP A 262 " model vdw 2.087 3.040 nonbonded pdb=" O THR B 261 " pdb=" OD1 ASP B 262 " model vdw 2.087 3.040 nonbonded pdb=" CD LYS B 258 " pdb=" CE1 PHE B 336 " model vdw 2.097 2.992 ... (remaining 52296 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 4.460 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.620 Find NCS groups from input model: 0.070 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:9.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 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 0.352 6476 Z= 0.700 Angle : 1.456 37.854 8810 Z= 1.001 Chirality : 0.100 1.311 968 Planarity : 0.019 0.280 1070 Dihedral : 16.084 81.389 2222 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.12 % Favored : 94.61 % Rotamer: Outliers : 2.41 % Allowed : 18.67 % Favored : 78.92 % Cbeta Deviations : 1.40 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.31), residues: 742 helix: 2.11 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -2.29 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 468 TYR 0.020 0.002 TYR A 368 PHE 0.039 0.002 PHE B 394 TRP 0.017 0.002 TRP B 607 HIS 0.002 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 6474) covalent geometry : angle 1.45569 ( 8810) hydrogen bonds : bond 0.10970 ( 451) hydrogen bonds : angle 5.20112 ( 1353) Misc. bond : bond 0.35193 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.249 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 80 average time/residue: 0.5213 time to fit residues: 43.8397 Evaluate side-chains 72 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 575 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.193743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.183584 restraints weight = 4895.569| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 0.35 r_work: 0.3771 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6476 Z= 0.231 Angle : 0.701 8.022 8810 Z= 0.382 Chirality : 0.048 0.159 968 Planarity : 0.007 0.057 1070 Dihedral : 7.248 56.843 860 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.23 % Favored : 96.50 % Rotamer: Outliers : 3.92 % Allowed : 19.28 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.30), residues: 742 helix: 1.94 (0.20), residues: 566 sheet: None (None), residues: 0 loop : -1.83 (0.48), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 548 TYR 0.020 0.003 TYR B 483 PHE 0.018 0.002 PHE B 394 TRP 0.018 0.003 TRP B 514 HIS 0.005 0.002 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 6474) covalent geometry : angle 0.70069 ( 8810) hydrogen bonds : bond 0.07037 ( 451) hydrogen bonds : angle 4.56093 ( 1353) Misc. bond : bond 0.00026 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.151 Fit side-chains REVERT: A 314 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7499 (mm-40) REVERT: A 543 GLU cc_start: 0.5288 (OUTLIER) cc_final: 0.5012 (mp0) REVERT: A 548 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7511 (ptt90) REVERT: B 314 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7488 (mm-40) REVERT: B 543 GLU cc_start: 0.5286 (OUTLIER) cc_final: 0.5009 (mp0) REVERT: B 548 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7512 (ptt90) outliers start: 26 outliers final: 14 residues processed: 82 average time/residue: 0.5665 time to fit residues: 48.5877 Evaluate side-chains 76 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 548 ARG Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 575 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 73 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 52 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 48 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.196903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.186670 restraints weight = 4872.761| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 0.34 r_work: 0.3799 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6476 Z= 0.143 Angle : 0.544 6.234 8810 Z= 0.296 Chirality : 0.040 0.140 968 Planarity : 0.005 0.053 1070 Dihedral : 6.031 56.277 844 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.92 % Allowed : 19.28 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.31), residues: 742 helix: 2.19 (0.20), residues: 580 sheet: None (None), residues: 0 loop : -1.53 (0.52), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 548 TYR 0.014 0.002 TYR A 368 PHE 0.013 0.002 PHE A 517 TRP 0.018 0.002 TRP A 607 HIS 0.002 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6474) covalent geometry : angle 0.54380 ( 8810) hydrogen bonds : bond 0.05522 ( 451) hydrogen bonds : angle 4.18884 ( 1353) Misc. bond : bond 0.00034 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.236 Fit side-chains REVERT: A 543 GLU cc_start: 0.5079 (OUTLIER) cc_final: 0.4779 (mp0) REVERT: B 543 GLU cc_start: 0.5080 (OUTLIER) cc_final: 0.4781 (mp0) outliers start: 26 outliers final: 14 residues processed: 84 average time/residue: 0.5773 time to fit residues: 50.7922 Evaluate side-chains 70 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 545 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 3 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.193669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.184958 restraints weight = 4846.014| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 0.31 r_work: 0.3787 rms_B_bonded: 0.93 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 1.56 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6476 Z= 0.191 Angle : 0.615 6.404 8810 Z= 0.337 Chirality : 0.045 0.151 968 Planarity : 0.006 0.050 1070 Dihedral : 5.942 44.914 840 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.92 % Allowed : 19.58 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.30), residues: 742 helix: 1.99 (0.20), residues: 580 sheet: None (None), residues: 0 loop : -1.75 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 548 TYR 0.019 0.002 TYR B 368 PHE 0.014 0.002 PHE B 394 TRP 0.017 0.002 TRP A 514 HIS 0.003 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 6474) covalent geometry : angle 0.61465 ( 8810) hydrogen bonds : bond 0.06512 ( 451) hydrogen bonds : angle 4.33650 ( 1353) Misc. bond : bond 0.00031 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.239 Fit side-chains REVERT: A 543 GLU cc_start: 0.5249 (OUTLIER) cc_final: 0.4892 (mp0) REVERT: B 543 GLU cc_start: 0.5244 (OUTLIER) cc_final: 0.4889 (mp0) outliers start: 26 outliers final: 12 residues processed: 78 average time/residue: 0.5209 time to fit residues: 42.8805 Evaluate side-chains 72 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 545 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 8 optimal weight: 0.0980 chunk 51 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 40 optimal weight: 0.0270 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 7 optimal weight: 0.1980 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.198504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.190282 restraints weight = 4969.407| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 0.32 r_work: 0.3841 rms_B_bonded: 0.93 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6476 Z= 0.128 Angle : 0.507 5.136 8810 Z= 0.275 Chirality : 0.039 0.135 968 Planarity : 0.004 0.047 1070 Dihedral : 5.493 44.489 840 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.31 % Allowed : 20.48 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.30 (0.31), residues: 742 helix: 2.37 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -1.72 (0.48), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 548 TYR 0.019 0.001 TYR A 368 PHE 0.013 0.001 PHE B 460 TRP 0.018 0.002 TRP A 607 HIS 0.001 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 6474) covalent geometry : angle 0.50684 ( 8810) hydrogen bonds : bond 0.05001 ( 451) hydrogen bonds : angle 4.04471 ( 1353) Misc. bond : bond 0.00023 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.249 Fit side-chains REVERT: A 543 GLU cc_start: 0.5044 (OUTLIER) cc_final: 0.4622 (mp0) REVERT: B 543 GLU cc_start: 0.5046 (OUTLIER) cc_final: 0.4622 (mp0) outliers start: 22 outliers final: 8 residues processed: 88 average time/residue: 0.5758 time to fit residues: 53.2258 Evaluate side-chains 72 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 575 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 66 optimal weight: 0.0670 chunk 25 optimal weight: 0.0770 chunk 44 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.197781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.188522 restraints weight = 4867.762| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 0.34 r_work: 0.3816 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 1.73 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 6476 Z= 0.131 Angle : 0.521 8.591 8810 Z= 0.278 Chirality : 0.039 0.138 968 Planarity : 0.004 0.046 1070 Dihedral : 5.306 41.265 836 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.01 % Allowed : 21.08 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.30), residues: 742 helix: 2.48 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -1.63 (0.48), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 448 TYR 0.020 0.002 TYR A 368 PHE 0.012 0.001 PHE B 610 TRP 0.016 0.002 TRP B 607 HIS 0.002 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6474) covalent geometry : angle 0.52145 ( 8810) hydrogen bonds : bond 0.05006 ( 451) hydrogen bonds : angle 3.99632 ( 1353) Misc. bond : bond 0.00022 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.256 Fit side-chains REVERT: A 543 GLU cc_start: 0.5059 (OUTLIER) cc_final: 0.4489 (mp0) REVERT: B 543 GLU cc_start: 0.5057 (OUTLIER) cc_final: 0.4487 (mp0) outliers start: 20 outliers final: 8 residues processed: 86 average time/residue: 0.6214 time to fit residues: 55.9728 Evaluate side-chains 73 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 545 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 29 optimal weight: 0.0870 chunk 32 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 0.0970 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.196974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.187682 restraints weight = 4844.399| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 0.34 r_work: 0.3808 rms_B_bonded: 1.04 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6476 Z= 0.139 Angle : 0.537 7.825 8810 Z= 0.289 Chirality : 0.040 0.137 968 Planarity : 0.004 0.045 1070 Dihedral : 5.351 40.605 836 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.71 % Allowed : 21.08 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.30), residues: 742 helix: 2.48 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -1.67 (0.48), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 448 TYR 0.022 0.002 TYR B 368 PHE 0.012 0.001 PHE B 610 TRP 0.015 0.002 TRP A 607 HIS 0.002 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6474) covalent geometry : angle 0.53707 ( 8810) hydrogen bonds : bond 0.05198 ( 451) hydrogen bonds : angle 4.06038 ( 1353) Misc. bond : bond 0.00017 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.255 Fit side-chains REVERT: A 543 GLU cc_start: 0.5123 (OUTLIER) cc_final: 0.4564 (mp0) REVERT: B 543 GLU cc_start: 0.5123 (OUTLIER) cc_final: 0.4564 (mp0) outliers start: 18 outliers final: 10 residues processed: 82 average time/residue: 0.6660 time to fit residues: 57.0195 Evaluate side-chains 74 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 575 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 28 optimal weight: 0.1980 chunk 33 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 7 optimal weight: 0.0020 chunk 49 optimal weight: 2.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.198181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.189380 restraints weight = 4908.123| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 0.33 r_work: 0.3829 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 1.68 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6476 Z= 0.128 Angle : 0.516 7.599 8810 Z= 0.275 Chirality : 0.039 0.136 968 Planarity : 0.004 0.045 1070 Dihedral : 5.242 39.202 836 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.01 % Allowed : 20.48 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.30), residues: 742 helix: 2.54 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -1.71 (0.48), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 448 TYR 0.024 0.002 TYR B 368 PHE 0.012 0.001 PHE B 610 TRP 0.015 0.002 TRP A 607 HIS 0.003 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 6474) covalent geometry : angle 0.51646 ( 8810) hydrogen bonds : bond 0.04961 ( 451) hydrogen bonds : angle 4.02208 ( 1353) Misc. bond : bond 0.00016 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.200 Fit side-chains REVERT: A 543 GLU cc_start: 0.5004 (OUTLIER) cc_final: 0.4439 (mp0) REVERT: B 543 GLU cc_start: 0.5003 (OUTLIER) cc_final: 0.4439 (mp0) outliers start: 20 outliers final: 10 residues processed: 84 average time/residue: 0.6383 time to fit residues: 55.9768 Evaluate side-chains 76 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 575 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 53 optimal weight: 0.9980 chunk 56 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 0.0060 chunk 47 optimal weight: 0.5980 chunk 45 optimal weight: 0.0980 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.198007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.187575 restraints weight = 4845.514| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 0.37 r_work: 0.3818 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3761 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6476 Z= 0.130 Angle : 0.519 7.469 8810 Z= 0.277 Chirality : 0.040 0.137 968 Planarity : 0.004 0.044 1070 Dihedral : 5.231 38.132 836 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.01 % Allowed : 20.78 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.54 (0.30), residues: 742 helix: 2.56 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -1.72 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 448 TYR 0.025 0.002 TYR A 368 PHE 0.012 0.001 PHE A 610 TRP 0.015 0.002 TRP B 607 HIS 0.002 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6474) covalent geometry : angle 0.51865 ( 8810) hydrogen bonds : bond 0.04990 ( 451) hydrogen bonds : angle 4.02436 ( 1353) Misc. bond : bond 0.00018 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.240 Fit side-chains REVERT: A 543 GLU cc_start: 0.5024 (OUTLIER) cc_final: 0.4482 (mp0) REVERT: B 543 GLU cc_start: 0.5024 (OUTLIER) cc_final: 0.4481 (mp0) outliers start: 20 outliers final: 10 residues processed: 84 average time/residue: 0.6566 time to fit residues: 57.7127 Evaluate side-chains 76 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 575 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 21 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.0020 chunk 9 optimal weight: 0.0870 chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 overall best weight: 0.4366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.198093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.183123 restraints weight = 4793.526| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 0.48 r_work: 0.3768 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6476 Z= 0.135 Angle : 0.532 7.489 8810 Z= 0.284 Chirality : 0.040 0.139 968 Planarity : 0.004 0.045 1070 Dihedral : 5.252 37.592 836 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.41 % Allowed : 21.39 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.30), residues: 742 helix: 2.52 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -1.75 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 448 TYR 0.027 0.002 TYR A 368 PHE 0.012 0.001 PHE A 610 TRP 0.015 0.002 TRP A 514 HIS 0.002 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6474) covalent geometry : angle 0.53183 ( 8810) hydrogen bonds : bond 0.05149 ( 451) hydrogen bonds : angle 4.06049 ( 1353) Misc. bond : bond 0.00014 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.243 Fit side-chains REVERT: A 543 GLU cc_start: 0.5210 (OUTLIER) cc_final: 0.4671 (mp0) REVERT: B 543 GLU cc_start: 0.5204 (OUTLIER) cc_final: 0.4665 (mp0) outliers start: 16 outliers final: 10 residues processed: 80 average time/residue: 0.6503 time to fit residues: 54.3159 Evaluate side-chains 76 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 575 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 7 optimal weight: 0.0570 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.199092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.174764 restraints weight = 4814.460| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 0.89 r_work: 0.3596 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6476 Z= 0.156 Angle : 0.566 7.719 8810 Z= 0.305 Chirality : 0.042 0.147 968 Planarity : 0.004 0.045 1070 Dihedral : 5.440 39.535 836 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.41 % Allowed : 21.08 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.30 (0.30), residues: 742 helix: 2.38 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -1.77 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 448 TYR 0.030 0.002 TYR A 368 PHE 0.012 0.002 PHE A 391 TRP 0.016 0.002 TRP A 514 HIS 0.002 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6474) covalent geometry : angle 0.56559 ( 8810) hydrogen bonds : bond 0.05671 ( 451) hydrogen bonds : angle 4.16337 ( 1353) Misc. bond : bond 0.00021 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2426.31 seconds wall clock time: 42 minutes 0.85 seconds (2520.85 seconds total)