Starting phenix.real_space_refine on Mon May 12 04:51:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bc1_15959/05_2025/8bc1_15959.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bc1_15959/05_2025/8bc1_15959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bc1_15959/05_2025/8bc1_15959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bc1_15959/05_2025/8bc1_15959.map" model { file = "/net/cci-nas-00/data/ceres_data/8bc1_15959/05_2025/8bc1_15959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bc1_15959/05_2025/8bc1_15959.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.001 sd= 0.019 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: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 62 5.16 5 C 5758 2.51 5 N 1366 2.21 5 O 1492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8684 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4339 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 6 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 7.82, per 1000 atoms: 0.90 Number of scatterers: 8684 At special positions: 0 Unit cell: (123.69, 79.422, 98.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 62 16.00 O 1492 8.00 N 1366 7.00 C 5758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 1.0 seconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2000 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 74.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 276 through 281 removed outlier: 4.612A pdb=" N TYR A 280 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 293 through 328 removed outlier: 3.619A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.648A pdb=" N ILE A 363 " --> pdb=" O ARG A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 376 through 409 removed outlier: 3.671A pdb=" N LEU A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 removed outlier: 3.697A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 487 removed outlier: 4.235A pdb=" N ILE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 539 removed outlier: 3.924A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 4.760A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 639 Proline residue: A 628 - end of helix removed outlier: 3.687A pdb=" N ARG A 639 " --> pdb=" O GLY A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 removed outlier: 3.513A pdb=" N HIS A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 681 removed outlier: 3.780A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.659A pdb=" N LEU A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 4.159A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 796 through 802 removed outlier: 4.416A pdb=" N GLY A 800 " --> pdb=" O ASN A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 removed outlier: 3.553A pdb=" N TRP A 829 " --> pdb=" O ASN A 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 272 Processing helix chain 'B' and resid 276 through 281 removed outlier: 4.614A pdb=" N TYR B 280 " --> pdb=" O ARG B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 292 Processing helix chain 'B' and resid 293 through 328 removed outlier: 3.619A pdb=" N LEU B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 338 Processing helix chain 'B' and resid 342 through 346 Processing helix chain 'B' and resid 360 through 363 removed outlier: 3.647A pdb=" N ILE B 363 " --> pdb=" O ARG B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 364 through 372 Processing helix chain 'B' and resid 376 through 409 removed outlier: 3.672A pdb=" N LEU B 394 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU B 395 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 426 removed outlier: 3.696A pdb=" N GLN B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 487 removed outlier: 4.234A pdb=" N ILE B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 539 removed outlier: 3.923A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 4.760A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 639 Proline residue: B 628 - end of helix removed outlier: 3.687A pdb=" N ARG B 639 " --> pdb=" O GLY B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 655 removed outlier: 3.513A pdb=" N HIS B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 681 removed outlier: 3.780A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.660A pdb=" N LEU B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 746 removed outlier: 4.159A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 796 through 802 removed outlier: 4.417A pdb=" N GLY B 800 " --> pdb=" O ASN B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 removed outlier: 3.552A pdb=" N TRP B 829 " --> pdb=" O ASN B 825 " (cutoff:3.500A) 579 hydrogen bonds defined for protein. 1713 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: 2.37 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2590 1.35 - 1.46: 2389 1.46 - 1.58: 3853 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 8928 Sorted by residual: bond pdb=" CA VAL B 411 " pdb=" CB VAL B 411 " ideal model delta sigma weight residual 1.530 1.541 -0.010 1.05e-02 9.07e+03 9.92e-01 bond pdb=" CA VAL A 411 " pdb=" CB VAL A 411 " ideal model delta sigma weight residual 1.530 1.540 -0.010 1.05e-02 9.07e+03 8.51e-01 bond pdb=" CA ILE B 751 " pdb=" CB ILE B 751 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.43e-01 bond pdb=" CA ILE A 700 " pdb=" C ILE A 700 " ideal model delta sigma weight residual 1.524 1.514 0.010 1.22e-02 6.72e+03 6.40e-01 bond pdb=" CA PHE A 685 " pdb=" CB PHE A 685 " ideal model delta sigma weight residual 1.532 1.544 -0.013 1.67e-02 3.59e+03 6.00e-01 ... (remaining 8923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 11780 1.11 - 2.22: 263 2.22 - 3.32: 71 3.32 - 4.43: 8 4.43 - 5.54: 8 Bond angle restraints: 12130 Sorted by residual: angle pdb=" N PRO A 763 " pdb=" CA PRO A 763 " pdb=" C PRO A 763 " ideal model delta sigma weight residual 110.70 113.26 -2.56 1.22e+00 6.72e-01 4.40e+00 angle pdb=" N PRO B 763 " pdb=" CA PRO B 763 " pdb=" C PRO B 763 " ideal model delta sigma weight residual 110.70 113.23 -2.53 1.22e+00 6.72e-01 4.29e+00 angle pdb=" C TYR B 580 " pdb=" CA TYR B 580 " pdb=" CB TYR B 580 " ideal model delta sigma weight residual 109.22 112.23 -3.01 1.52e+00 4.33e-01 3.92e+00 angle pdb=" C TYR A 580 " pdb=" CA TYR A 580 " pdb=" CB TYR A 580 " ideal model delta sigma weight residual 109.22 112.20 -2.98 1.52e+00 4.33e-01 3.85e+00 angle pdb=" CA PRO B 763 " pdb=" C PRO B 763 " pdb=" N PRO B 764 " ideal model delta sigma weight residual 117.93 120.18 -2.25 1.20e+00 6.94e-01 3.51e+00 ... (remaining 12125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.66: 4748 12.66 - 25.33: 336 25.33 - 37.99: 96 37.99 - 50.65: 32 50.65 - 63.31: 8 Dihedral angle restraints: 5220 sinusoidal: 2106 harmonic: 3114 Sorted by residual: dihedral pdb=" CA VAL A 625 " pdb=" C VAL A 625 " pdb=" N LEU A 626 " pdb=" CA LEU A 626 " ideal model delta harmonic sigma weight residual -180.00 -164.06 -15.94 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA VAL B 625 " pdb=" C VAL B 625 " pdb=" N LEU B 626 " pdb=" CA LEU B 626 " ideal model delta harmonic sigma weight residual -180.00 -164.07 -15.93 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" N GLU B 395 " pdb=" CA GLU B 395 " pdb=" CB GLU B 395 " pdb=" CG GLU B 395 " ideal model delta sinusoidal sigma weight residual -60.00 -117.63 57.63 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 5217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 812 0.025 - 0.050: 276 0.050 - 0.075: 173 0.075 - 0.100: 63 0.100 - 0.125: 8 Chirality restraints: 1332 Sorted by residual: chirality pdb=" CA VAL B 715 " pdb=" N VAL B 715 " pdb=" C VAL B 715 " pdb=" CB VAL B 715 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA VAL A 715 " pdb=" N VAL A 715 " pdb=" C VAL A 715 " pdb=" CB VAL A 715 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA PRO A 689 " pdb=" N PRO A 689 " pdb=" C PRO A 689 " pdb=" CB PRO A 689 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.05e-01 ... (remaining 1329 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 700 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" C ILE A 700 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE A 700 " -0.009 2.00e-02 2.50e+03 pdb=" N ARG A 701 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 697 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.03e+00 pdb=" C ILE B 697 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE B 697 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU B 698 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 697 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C ILE A 697 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE A 697 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU A 698 " -0.008 2.00e-02 2.50e+03 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2201 2.79 - 3.32: 9052 3.32 - 3.85: 14674 3.85 - 4.37: 16711 4.37 - 4.90: 28388 Nonbonded interactions: 71026 Sorted by model distance: nonbonded pdb=" O LEU B 626 " pdb=" N VAL B 630 " model vdw 2.265 3.120 nonbonded pdb=" O LEU A 626 " pdb=" N VAL A 630 " model vdw 2.265 3.120 nonbonded pdb=" O THR B 364 " pdb=" OG SER B 367 " model vdw 2.273 3.040 nonbonded pdb=" O THR A 364 " pdb=" OG SER A 367 " model vdw 2.273 3.040 nonbonded pdb=" O SER A 376 " pdb=" OG1 THR A 379 " model vdw 2.281 3.040 ... (remaining 71021 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: 0.04 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.350 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:12.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5220 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 : 0.002 0.018 8936 Z= 0.112 Angle : 0.458 5.542 12146 Z= 0.261 Chirality : 0.036 0.125 1332 Planarity : 0.004 0.032 1486 Dihedral : 10.381 63.314 3196 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.43 % Allowed : 5.25 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.26), residues: 1026 helix: 1.62 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -0.51 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 397 HIS 0.002 0.001 HIS A 830 PHE 0.011 0.001 PHE B 393 TYR 0.011 0.001 TYR A 580 ARG 0.002 0.000 ARG B 592 Details of bonding type rmsd hydrogen bonds : bond 0.10487 ( 579) hydrogen bonds : angle 5.31130 ( 1713) SS BOND : bond 0.00181 ( 8) SS BOND : angle 0.74170 ( 16) covalent geometry : bond 0.00194 ( 8928) covalent geometry : angle 0.45784 (12130) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 252 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 LEU cc_start: 0.8370 (mt) cc_final: 0.8006 (tp) REVERT: A 381 ILE cc_start: 0.6080 (mt) cc_final: 0.5828 (mt) REVERT: A 386 MET cc_start: 0.5095 (mmp) cc_final: 0.4500 (mmp) REVERT: A 530 LYS cc_start: 0.6932 (mmtm) cc_final: 0.6593 (mmmm) REVERT: A 595 GLU cc_start: 0.5110 (mp0) cc_final: 0.3651 (tm-30) REVERT: A 613 MET cc_start: 0.6979 (mtp) cc_final: 0.6312 (mtp) REVERT: A 638 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7104 (tmmt) REVERT: A 813 ARG cc_start: 0.4596 (mtt90) cc_final: 0.3334 (ppt170) REVERT: B 285 LEU cc_start: 0.8377 (mt) cc_final: 0.8019 (tp) REVERT: B 381 ILE cc_start: 0.6065 (mt) cc_final: 0.5805 (mt) REVERT: B 386 MET cc_start: 0.5120 (mmp) cc_final: 0.4486 (mmp) REVERT: B 507 MET cc_start: 0.5033 (ttm) cc_final: 0.4176 (tpp) REVERT: B 530 LYS cc_start: 0.6927 (mmtm) cc_final: 0.6587 (mmmm) REVERT: B 595 GLU cc_start: 0.5123 (mp0) cc_final: 0.3668 (tm-30) REVERT: B 613 MET cc_start: 0.6980 (mtp) cc_final: 0.6311 (mtp) REVERT: B 638 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7140 (tmmt) REVERT: B 813 ARG cc_start: 0.4723 (mtt90) cc_final: 0.3329 (ppt170) outliers start: 32 outliers final: 3 residues processed: 280 average time/residue: 0.8279 time to fit residues: 251.7517 Evaluate side-chains 170 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 165 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 0.0020 chunk 26 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN A 559 GLN A 632 ASN A 730 GLN A 814 ASN A 830 HIS B 401 GLN B 559 GLN B 632 ASN B 730 GLN B 814 ASN B 830 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5248 r_free = 0.5248 target = 0.269951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5053 r_free = 0.5053 target = 0.248772 restraints weight = 14181.461| |-----------------------------------------------------------------------------| r_work (start): 0.5061 rms_B_bonded: 2.60 r_work: 0.4973 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5307 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8936 Z= 0.161 Angle : 0.654 10.985 12146 Z= 0.338 Chirality : 0.042 0.163 1332 Planarity : 0.005 0.045 1486 Dihedral : 4.291 42.945 1172 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.64 % Allowed : 14.88 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.26), residues: 1026 helix: 1.61 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.41 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 408 HIS 0.020 0.002 HIS B 844 PHE 0.013 0.001 PHE B 558 TYR 0.015 0.001 TYR A 668 ARG 0.004 0.001 ARG B 592 Details of bonding type rmsd hydrogen bonds : bond 0.04743 ( 579) hydrogen bonds : angle 4.66450 ( 1713) SS BOND : bond 0.00425 ( 8) SS BOND : angle 2.72010 ( 16) covalent geometry : bond 0.00367 ( 8928) covalent geometry : angle 0.64673 (12130) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 381 ILE cc_start: 0.6327 (mt) cc_final: 0.6039 (mt) REVERT: A 553 MET cc_start: 0.6824 (tmt) cc_final: 0.6368 (tmm) REVERT: A 595 GLU cc_start: 0.4781 (mp0) cc_final: 0.3304 (tm-30) REVERT: A 613 MET cc_start: 0.7006 (mtp) cc_final: 0.6284 (ttm) REVERT: A 638 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7071 (tmmt) REVERT: A 813 ARG cc_start: 0.4741 (mtt90) cc_final: 0.3252 (ppt170) REVERT: B 381 ILE cc_start: 0.6369 (mt) cc_final: 0.6078 (mt) REVERT: B 553 MET cc_start: 0.6810 (tmt) cc_final: 0.6357 (tmm) REVERT: B 595 GLU cc_start: 0.4798 (mp0) cc_final: 0.3322 (tm-30) REVERT: B 613 MET cc_start: 0.6993 (mtp) cc_final: 0.6301 (ttm) REVERT: B 638 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7085 (tmmt) REVERT: B 813 ARG cc_start: 0.4800 (mtt90) cc_final: 0.3312 (ppt170) outliers start: 34 outliers final: 8 residues processed: 205 average time/residue: 0.9576 time to fit residues: 212.8188 Evaluate side-chains 148 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 840 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN B 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5222 r_free = 0.5222 target = 0.266733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5021 r_free = 0.5021 target = 0.245402 restraints weight = 14169.428| |-----------------------------------------------------------------------------| r_work (start): 0.5012 rms_B_bonded: 2.73 r_work: 0.4918 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5326 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 8936 Z= 0.165 Angle : 0.657 9.658 12146 Z= 0.334 Chirality : 0.041 0.145 1332 Planarity : 0.005 0.049 1486 Dihedral : 4.439 42.264 1172 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.18 % Allowed : 18.31 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.25), residues: 1026 helix: 1.51 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.62 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 408 HIS 0.013 0.002 HIS A 844 PHE 0.025 0.001 PHE A 558 TYR 0.015 0.001 TYR B 528 ARG 0.017 0.001 ARG B 810 Details of bonding type rmsd hydrogen bonds : bond 0.04579 ( 579) hydrogen bonds : angle 4.56552 ( 1713) SS BOND : bond 0.00467 ( 8) SS BOND : angle 2.73503 ( 16) covalent geometry : bond 0.00372 ( 8928) covalent geometry : angle 0.65006 (12130) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 366 GLU cc_start: 0.5920 (tp30) cc_final: 0.5686 (tp30) REVERT: A 381 ILE cc_start: 0.6409 (mt) cc_final: 0.6119 (mt) REVERT: A 553 MET cc_start: 0.6688 (tmt) cc_final: 0.6182 (tmm) REVERT: A 595 GLU cc_start: 0.4960 (mp0) cc_final: 0.3420 (tm-30) REVERT: A 604 GLU cc_start: 0.7583 (tm-30) cc_final: 0.6946 (mt-10) REVERT: A 613 MET cc_start: 0.7198 (mtp) cc_final: 0.6492 (mtp) REVERT: A 638 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7170 (tmmt) REVERT: A 813 ARG cc_start: 0.4739 (mtt90) cc_final: 0.3289 (ppt170) REVERT: B 294 GLU cc_start: 0.4665 (mm-30) cc_final: 0.4255 (mp0) REVERT: B 310 LEU cc_start: 0.5191 (mt) cc_final: 0.4894 (mt) REVERT: B 381 ILE cc_start: 0.6404 (mt) cc_final: 0.6115 (mt) REVERT: B 553 MET cc_start: 0.6670 (tmt) cc_final: 0.6172 (tmm) REVERT: B 595 GLU cc_start: 0.4950 (mp0) cc_final: 0.3415 (tm-30) REVERT: B 604 GLU cc_start: 0.7437 (tm-30) cc_final: 0.6789 (mt-10) REVERT: B 613 MET cc_start: 0.7201 (mtp) cc_final: 0.6637 (mtp) REVERT: B 638 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7207 (tmmt) REVERT: B 813 ARG cc_start: 0.4885 (mtt90) cc_final: 0.3305 (ppt170) outliers start: 39 outliers final: 17 residues processed: 193 average time/residue: 0.8261 time to fit residues: 174.0046 Evaluate side-chains 164 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 14 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 549 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5217 r_free = 0.5217 target = 0.266360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5011 r_free = 0.5011 target = 0.245002 restraints weight = 14169.059| |-----------------------------------------------------------------------------| r_work (start): 0.5006 rms_B_bonded: 2.64 r_work: 0.4910 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5418 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8936 Z= 0.170 Angle : 0.687 13.421 12146 Z= 0.339 Chirality : 0.042 0.162 1332 Planarity : 0.005 0.050 1486 Dihedral : 4.439 41.241 1172 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.57 % Allowed : 17.24 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.25), residues: 1026 helix: 1.38 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.70 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 408 HIS 0.008 0.001 HIS A 844 PHE 0.028 0.002 PHE A 558 TYR 0.018 0.001 TYR A 528 ARG 0.007 0.001 ARG B 810 Details of bonding type rmsd hydrogen bonds : bond 0.04663 ( 579) hydrogen bonds : angle 4.64335 ( 1713) SS BOND : bond 0.00450 ( 8) SS BOND : angle 3.30133 ( 16) covalent geometry : bond 0.00380 ( 8928) covalent geometry : angle 0.67668 (12130) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 165 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6948 (tmt90) REVERT: A 381 ILE cc_start: 0.6385 (mt) cc_final: 0.6075 (mt) REVERT: A 553 MET cc_start: 0.6776 (tmt) cc_final: 0.6253 (tmm) REVERT: A 595 GLU cc_start: 0.4862 (mp0) cc_final: 0.3357 (tm-30) REVERT: A 604 GLU cc_start: 0.7555 (tm-30) cc_final: 0.6952 (mt-10) REVERT: A 608 GLN cc_start: 0.6171 (tp40) cc_final: 0.5336 (tt0) REVERT: A 613 MET cc_start: 0.6977 (mtp) cc_final: 0.6402 (mtp) REVERT: A 638 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7211 (tmmt) REVERT: A 699 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6944 (tp30) REVERT: A 813 ARG cc_start: 0.4857 (mtt90) cc_final: 0.3280 (ppt170) REVERT: B 289 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6927 (tmt90) REVERT: B 381 ILE cc_start: 0.6395 (mt) cc_final: 0.6078 (mt) REVERT: B 553 MET cc_start: 0.6809 (tmt) cc_final: 0.6503 (tmt) REVERT: B 595 GLU cc_start: 0.4847 (mp0) cc_final: 0.3351 (tm-30) REVERT: B 604 GLU cc_start: 0.7481 (tm-30) cc_final: 0.6897 (mt-10) REVERT: B 613 MET cc_start: 0.7057 (mtp) cc_final: 0.6471 (mtp) REVERT: B 638 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7233 (tmmt) REVERT: B 699 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6952 (tp30) REVERT: B 813 ARG cc_start: 0.4851 (mtt90) cc_final: 0.3197 (ppt170) outliers start: 52 outliers final: 17 residues processed: 200 average time/residue: 0.7948 time to fit residues: 173.9834 Evaluate side-chains 169 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 64 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5211 r_free = 0.5211 target = 0.266216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.244567 restraints weight = 14250.901| |-----------------------------------------------------------------------------| r_work (start): 0.5001 rms_B_bonded: 2.67 r_work: 0.4906 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5419 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 8936 Z= 0.163 Angle : 0.701 13.083 12146 Z= 0.348 Chirality : 0.042 0.154 1332 Planarity : 0.005 0.052 1486 Dihedral : 4.422 41.456 1170 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.93 % Allowed : 19.59 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.26), residues: 1026 helix: 1.32 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.75 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 408 HIS 0.005 0.001 HIS A 844 PHE 0.032 0.002 PHE A 558 TYR 0.019 0.001 TYR B 306 ARG 0.003 0.001 ARG A 649 Details of bonding type rmsd hydrogen bonds : bond 0.04622 ( 579) hydrogen bonds : angle 4.62802 ( 1713) SS BOND : bond 0.00340 ( 8) SS BOND : angle 1.61454 ( 16) covalent geometry : bond 0.00369 ( 8928) covalent geometry : angle 0.69877 (12130) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 0.877 Fit side-chains REVERT: A 289 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.6907 (tmt90) REVERT: A 294 GLU cc_start: 0.4754 (mm-30) cc_final: 0.4488 (mp0) REVERT: A 381 ILE cc_start: 0.6411 (mt) cc_final: 0.6117 (mt) REVERT: A 534 MET cc_start: 0.6790 (mmt) cc_final: 0.6532 (mmt) REVERT: A 553 MET cc_start: 0.6832 (tmt) cc_final: 0.6331 (tmm) REVERT: A 595 GLU cc_start: 0.4473 (mp0) cc_final: 0.3068 (tm-30) REVERT: A 604 GLU cc_start: 0.7526 (tm-30) cc_final: 0.6903 (mt-10) REVERT: A 613 MET cc_start: 0.7030 (mtp) cc_final: 0.6316 (mtp) REVERT: A 638 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7102 (tmmt) REVERT: A 699 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6856 (tp30) REVERT: A 813 ARG cc_start: 0.4887 (mtt90) cc_final: 0.3185 (ppt170) REVERT: B 294 GLU cc_start: 0.4729 (mm-30) cc_final: 0.4227 (mp0) REVERT: B 381 ILE cc_start: 0.6451 (mt) cc_final: 0.6151 (mt) REVERT: B 408 TRP cc_start: 0.6652 (m-10) cc_final: 0.6409 (m100) REVERT: B 534 MET cc_start: 0.6745 (mmt) cc_final: 0.6508 (mmt) REVERT: B 553 MET cc_start: 0.6847 (tmt) cc_final: 0.6343 (tmm) REVERT: B 595 GLU cc_start: 0.4631 (mp0) cc_final: 0.3044 (tm-30) REVERT: B 604 GLU cc_start: 0.7525 (tm-30) cc_final: 0.6908 (mt-10) REVERT: B 608 GLN cc_start: 0.6164 (tp40) cc_final: 0.5329 (tt0) REVERT: B 613 MET cc_start: 0.7030 (mtp) cc_final: 0.6322 (mtp) REVERT: B 638 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7204 (tmmt) REVERT: B 699 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6866 (tp30) REVERT: B 813 ARG cc_start: 0.4883 (mtt90) cc_final: 0.3176 (ppt170) outliers start: 46 outliers final: 16 residues processed: 190 average time/residue: 0.7835 time to fit residues: 163.0552 Evaluate side-chains 165 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 0.0970 chunk 78 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 61 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 67 optimal weight: 0.2980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 608 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5215 r_free = 0.5215 target = 0.266065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5018 r_free = 0.5018 target = 0.245159 restraints weight = 13887.824| |-----------------------------------------------------------------------------| r_work (start): 0.5057 rms_B_bonded: 2.66 r_work: 0.4978 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5372 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8936 Z= 0.149 Angle : 0.726 15.785 12146 Z= 0.354 Chirality : 0.042 0.152 1332 Planarity : 0.005 0.060 1486 Dihedral : 4.580 42.965 1170 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.43 % Allowed : 21.52 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1026 helix: 1.30 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.79 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 408 HIS 0.004 0.001 HIS B 844 PHE 0.031 0.001 PHE A 558 TYR 0.017 0.001 TYR A 528 ARG 0.007 0.001 ARG B 592 Details of bonding type rmsd hydrogen bonds : bond 0.04474 ( 579) hydrogen bonds : angle 4.64699 ( 1713) SS BOND : bond 0.00365 ( 8) SS BOND : angle 3.60390 ( 16) covalent geometry : bond 0.00335 ( 8928) covalent geometry : angle 0.71415 (12130) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 381 ILE cc_start: 0.6357 (mt) cc_final: 0.6074 (mt) REVERT: A 553 MET cc_start: 0.6775 (tmt) cc_final: 0.6263 (tmm) REVERT: A 595 GLU cc_start: 0.3706 (mp0) cc_final: 0.2478 (tm-30) REVERT: A 604 GLU cc_start: 0.7536 (tm-30) cc_final: 0.6886 (mt-10) REVERT: A 613 MET cc_start: 0.6793 (mtp) cc_final: 0.6219 (mtp) REVERT: A 638 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7129 (tmmt) REVERT: A 813 ARG cc_start: 0.4609 (mtt90) cc_final: 0.3079 (ppt170) REVERT: B 289 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7377 (tmt-80) REVERT: B 294 GLU cc_start: 0.4588 (mm-30) cc_final: 0.4360 (mp0) REVERT: B 381 ILE cc_start: 0.6398 (mt) cc_final: 0.6110 (mt) REVERT: B 553 MET cc_start: 0.6821 (tmt) cc_final: 0.6301 (tmm) REVERT: B 595 GLU cc_start: 0.3731 (mp0) cc_final: 0.2444 (tm-30) REVERT: B 604 GLU cc_start: 0.7475 (tm-30) cc_final: 0.6828 (mt-10) REVERT: B 608 GLN cc_start: 0.6022 (OUTLIER) cc_final: 0.5220 (tt0) REVERT: B 613 MET cc_start: 0.6923 (mtp) cc_final: 0.6351 (mtp) REVERT: B 638 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7168 (tmmt) REVERT: B 813 ARG cc_start: 0.4725 (mtt90) cc_final: 0.3098 (ppt170) outliers start: 32 outliers final: 13 residues processed: 179 average time/residue: 0.8519 time to fit residues: 167.1816 Evaluate side-chains 166 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 608 GLN Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 75 optimal weight: 2.9990 chunk 33 optimal weight: 0.0070 chunk 57 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 45 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.5209 r_free = 0.5209 target = 0.265823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.244222 restraints weight = 14439.900| |-----------------------------------------------------------------------------| r_work (start): 0.5034 rms_B_bonded: 2.74 r_work: 0.4931 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.4931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5385 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8936 Z= 0.149 Angle : 0.684 16.462 12146 Z= 0.339 Chirality : 0.042 0.158 1332 Planarity : 0.005 0.053 1486 Dihedral : 4.522 41.361 1170 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.68 % Allowed : 22.70 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1026 helix: 1.31 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.78 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 408 HIS 0.003 0.001 HIS B 844 PHE 0.033 0.001 PHE A 558 TYR 0.017 0.001 TYR A 528 ARG 0.007 0.000 ARG A 592 Details of bonding type rmsd hydrogen bonds : bond 0.04443 ( 579) hydrogen bonds : angle 4.67558 ( 1713) SS BOND : bond 0.00253 ( 8) SS BOND : angle 2.68773 ( 16) covalent geometry : bond 0.00334 ( 8928) covalent geometry : angle 0.67741 (12130) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 381 ILE cc_start: 0.6368 (mt) cc_final: 0.6077 (mt) REVERT: A 530 LYS cc_start: 0.6078 (mmtp) cc_final: 0.5708 (mptm) REVERT: A 534 MET cc_start: 0.6729 (mmt) cc_final: 0.6442 (mmt) REVERT: A 553 MET cc_start: 0.6814 (tmt) cc_final: 0.6309 (tmm) REVERT: A 595 GLU cc_start: 0.3725 (mp0) cc_final: 0.2452 (tm-30) REVERT: A 604 GLU cc_start: 0.7553 (tm-30) cc_final: 0.6876 (mt-10) REVERT: A 613 MET cc_start: 0.6947 (mtp) cc_final: 0.6397 (mtp) REVERT: A 638 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7149 (tmmt) REVERT: A 659 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.6369 (mtp) REVERT: A 813 ARG cc_start: 0.4812 (mtt90) cc_final: 0.3109 (ppt170) REVERT: B 289 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.7034 (ttt90) REVERT: B 381 ILE cc_start: 0.6416 (mt) cc_final: 0.6118 (mt) REVERT: B 530 LYS cc_start: 0.6086 (mmtp) cc_final: 0.5842 (mmtt) REVERT: B 553 MET cc_start: 0.6845 (tmt) cc_final: 0.6309 (tmm) REVERT: B 595 GLU cc_start: 0.3488 (mp0) cc_final: 0.2424 (tm-30) REVERT: B 604 GLU cc_start: 0.7333 (tm-30) cc_final: 0.6621 (mt-10) REVERT: B 613 MET cc_start: 0.7035 (mtp) cc_final: 0.6331 (mtp) REVERT: B 638 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7202 (tmmt) REVERT: B 813 ARG cc_start: 0.4613 (mtt90) cc_final: 0.3058 (ppt170) outliers start: 25 outliers final: 13 residues processed: 171 average time/residue: 0.7679 time to fit residues: 144.2164 Evaluate side-chains 161 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 84 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 0.0570 chunk 16 optimal weight: 9.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN A 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5204 r_free = 0.5204 target = 0.265062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5000 r_free = 0.5000 target = 0.243308 restraints weight = 14412.911| |-----------------------------------------------------------------------------| r_work (start): 0.5038 rms_B_bonded: 2.73 r_work: 0.4960 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5422 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8936 Z= 0.158 Angle : 0.692 16.460 12146 Z= 0.344 Chirality : 0.042 0.157 1332 Planarity : 0.005 0.054 1486 Dihedral : 4.548 40.394 1170 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.78 % Allowed : 23.23 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1026 helix: 1.30 (0.18), residues: 738 sheet: None (None), residues: 0 loop : -0.86 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP A 408 HIS 0.003 0.001 HIS B 844 PHE 0.034 0.002 PHE A 558 TYR 0.017 0.001 TYR A 528 ARG 0.007 0.000 ARG A 592 Details of bonding type rmsd hydrogen bonds : bond 0.04539 ( 579) hydrogen bonds : angle 4.71946 ( 1713) SS BOND : bond 0.00198 ( 8) SS BOND : angle 2.11359 ( 16) covalent geometry : bond 0.00354 ( 8928) covalent geometry : angle 0.68794 (12130) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 381 ILE cc_start: 0.6347 (mt) cc_final: 0.6073 (mt) REVERT: A 530 LYS cc_start: 0.6252 (mmtp) cc_final: 0.5903 (mptm) REVERT: A 553 MET cc_start: 0.6866 (tmt) cc_final: 0.6334 (tmm) REVERT: A 595 GLU cc_start: 0.3329 (mp0) cc_final: 0.2518 (tm-30) REVERT: A 604 GLU cc_start: 0.7431 (tm-30) cc_final: 0.6719 (mt-10) REVERT: A 613 MET cc_start: 0.6850 (mtp) cc_final: 0.6322 (mtp) REVERT: A 638 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7087 (tmmt) REVERT: A 699 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6873 (tp30) REVERT: A 813 ARG cc_start: 0.4683 (mtt90) cc_final: 0.3088 (ppt170) REVERT: B 289 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7110 (ttt90) REVERT: B 381 ILE cc_start: 0.6388 (mt) cc_final: 0.6120 (mt) REVERT: B 553 MET cc_start: 0.6901 (tmt) cc_final: 0.6352 (tmm) REVERT: B 555 MET cc_start: 0.7414 (mmm) cc_final: 0.7052 (tpt) REVERT: B 595 GLU cc_start: 0.3590 (mp0) cc_final: 0.2490 (tm-30) REVERT: B 604 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6591 (mt-10) REVERT: B 613 MET cc_start: 0.6897 (mtp) cc_final: 0.6351 (mtp) REVERT: B 638 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7176 (tmmt) REVERT: B 813 ARG cc_start: 0.4680 (mtt90) cc_final: 0.3126 (ppt170) outliers start: 26 outliers final: 11 residues processed: 161 average time/residue: 0.7722 time to fit residues: 137.1621 Evaluate side-chains 151 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 738 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 59 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5217 r_free = 0.5217 target = 0.267374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5011 r_free = 0.5011 target = 0.245517 restraints weight = 14308.691| |-----------------------------------------------------------------------------| r_work (start): 0.5007 rms_B_bonded: 2.75 r_work: 0.4907 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5424 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8936 Z= 0.171 Angle : 0.722 16.801 12146 Z= 0.359 Chirality : 0.045 0.308 1332 Planarity : 0.005 0.055 1486 Dihedral : 4.329 27.611 1166 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.57 % Allowed : 23.88 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.26), residues: 1026 helix: 1.20 (0.18), residues: 738 sheet: None (None), residues: 0 loop : -0.93 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.002 TRP A 408 HIS 0.003 0.001 HIS A 844 PHE 0.036 0.002 PHE A 558 TYR 0.018 0.001 TYR B 306 ARG 0.006 0.001 ARG A 592 Details of bonding type rmsd hydrogen bonds : bond 0.04627 ( 579) hydrogen bonds : angle 4.80588 ( 1713) SS BOND : bond 0.00185 ( 8) SS BOND : angle 1.85716 ( 16) covalent geometry : bond 0.00384 ( 8928) covalent geometry : angle 0.71930 (12130) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 381 ILE cc_start: 0.6393 (mt) cc_final: 0.6152 (mt) REVERT: A 530 LYS cc_start: 0.6166 (mmtp) cc_final: 0.5838 (mptm) REVERT: A 534 MET cc_start: 0.6742 (mmt) cc_final: 0.6499 (mmt) REVERT: A 553 MET cc_start: 0.6887 (tmt) cc_final: 0.6357 (tmm) REVERT: A 595 GLU cc_start: 0.3375 (mp0) cc_final: 0.2556 (tm-30) REVERT: A 604 GLU cc_start: 0.7410 (tm-30) cc_final: 0.6663 (mt-10) REVERT: A 613 MET cc_start: 0.6956 (mtp) cc_final: 0.6432 (mtp) REVERT: A 638 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7103 (tmmt) REVERT: A 813 ARG cc_start: 0.4786 (mtt90) cc_final: 0.3145 (ppt170) REVERT: A 842 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7386 (mpp) REVERT: B 289 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6684 (tmt90) REVERT: B 381 ILE cc_start: 0.6427 (mt) cc_final: 0.6210 (mt) REVERT: B 553 MET cc_start: 0.6916 (tmt) cc_final: 0.6369 (tmm) REVERT: B 595 GLU cc_start: 0.3147 (mp0) cc_final: 0.2303 (tm-30) REVERT: B 604 GLU cc_start: 0.7354 (tm-30) cc_final: 0.6558 (mp0) REVERT: B 613 MET cc_start: 0.6923 (mtp) cc_final: 0.6410 (mtp) REVERT: B 638 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7213 (tmmt) REVERT: B 659 MET cc_start: 0.6682 (mtm) cc_final: 0.6425 (mtp) REVERT: B 671 MET cc_start: 0.7699 (mmt) cc_final: 0.7356 (mmp) REVERT: B 813 ARG cc_start: 0.4789 (mtt90) cc_final: 0.3123 (ppt170) outliers start: 24 outliers final: 10 residues processed: 163 average time/residue: 0.7467 time to fit residues: 134.1501 Evaluate side-chains 148 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 738 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 79 optimal weight: 0.0570 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.0570 chunk 12 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- 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 = 0.5231 r_free = 0.5231 target = 0.269264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5032 r_free = 0.5032 target = 0.247705 restraints weight = 14279.988| |-----------------------------------------------------------------------------| r_work (start): 0.5020 rms_B_bonded: 2.74 r_work: 0.4921 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5369 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8936 Z= 0.154 Angle : 0.716 17.056 12146 Z= 0.357 Chirality : 0.044 0.264 1332 Planarity : 0.005 0.055 1486 Dihedral : 4.325 25.880 1166 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.93 % Allowed : 25.70 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.26), residues: 1026 helix: 1.17 (0.18), residues: 736 sheet: None (None), residues: 0 loop : -1.00 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP A 408 HIS 0.003 0.001 HIS A 844 PHE 0.038 0.002 PHE A 558 TYR 0.015 0.001 TYR A 528 ARG 0.006 0.000 ARG A 592 Details of bonding type rmsd hydrogen bonds : bond 0.04578 ( 579) hydrogen bonds : angle 4.81214 ( 1713) SS BOND : bond 0.00172 ( 8) SS BOND : angle 1.61971 ( 16) covalent geometry : bond 0.00337 ( 8928) covalent geometry : angle 0.71419 (12130) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 289 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.6853 (ttm-80) REVERT: A 381 ILE cc_start: 0.6372 (mt) cc_final: 0.6155 (mt) REVERT: A 408 TRP cc_start: 0.6281 (m100) cc_final: 0.6042 (m100) REVERT: A 468 ILE cc_start: 0.8565 (mm) cc_final: 0.8335 (pt) REVERT: A 530 LYS cc_start: 0.6160 (mmtp) cc_final: 0.5802 (mptm) REVERT: A 534 MET cc_start: 0.6700 (mmt) cc_final: 0.6439 (mmt) REVERT: A 553 MET cc_start: 0.6851 (tmt) cc_final: 0.6323 (tmm) REVERT: A 595 GLU cc_start: 0.3124 (mp0) cc_final: 0.2275 (tm-30) REVERT: A 604 GLU cc_start: 0.7398 (tm-30) cc_final: 0.6611 (mp0) REVERT: A 613 MET cc_start: 0.6895 (mtp) cc_final: 0.6366 (mtp) REVERT: A 638 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7168 (tmmt) REVERT: A 813 ARG cc_start: 0.5122 (mtt90) cc_final: 0.3191 (ppt170) REVERT: B 553 MET cc_start: 0.6869 (tmt) cc_final: 0.6323 (tmm) REVERT: B 595 GLU cc_start: 0.3155 (mp0) cc_final: 0.2285 (tm-30) REVERT: B 604 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6541 (mt-10) REVERT: B 613 MET cc_start: 0.6880 (mtp) cc_final: 0.6357 (mtp) REVERT: B 638 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7197 (tmmt) REVERT: B 671 MET cc_start: 0.7639 (mmt) cc_final: 0.7303 (mmt) REVERT: B 813 ARG cc_start: 0.5143 (mtt90) cc_final: 0.3179 (ppt170) REVERT: B 842 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7341 (mpp) outliers start: 18 outliers final: 12 residues processed: 156 average time/residue: 0.8092 time to fit residues: 138.3636 Evaluate side-chains 151 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 33 optimal weight: 0.0670 chunk 14 optimal weight: 0.0010 chunk 99 optimal weight: 0.0670 chunk 26 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 overall best weight: 0.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5238 r_free = 0.5238 target = 0.269538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5051 r_free = 0.5051 target = 0.247611 restraints weight = 13877.993| |-----------------------------------------------------------------------------| r_work (start): 0.5042 rms_B_bonded: 2.76 r_work: 0.4933 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5341 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8936 Z= 0.144 Angle : 0.718 17.109 12146 Z= 0.355 Chirality : 0.044 0.235 1332 Planarity : 0.005 0.056 1486 Dihedral : 4.325 24.506 1166 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.03 % Allowed : 26.02 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.26), residues: 1026 helix: 1.21 (0.18), residues: 736 sheet: None (None), residues: 0 loop : -0.97 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP A 408 HIS 0.002 0.001 HIS A 844 PHE 0.034 0.001 PHE A 558 TYR 0.015 0.001 TYR A 528 ARG 0.010 0.000 ARG B 289 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 579) hydrogen bonds : angle 4.77337 ( 1713) SS BOND : bond 0.00245 ( 8) SS BOND : angle 1.70640 ( 16) covalent geometry : bond 0.00315 ( 8928) covalent geometry : angle 0.71562 (12130) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5216.35 seconds wall clock time: 90 minutes 46.28 seconds (5446.28 seconds total)