Starting phenix.real_space_refine on Thu Feb 13 05:53:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bc1_15959/02_2025/8bc1_15959.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bc1_15959/02_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_15959/02_2025/8bc1_15959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bc1_15959/02_2025/8bc1_15959.map" model { file = "/net/cci-nas-00/data/ceres_data/8bc1_15959/02_2025/8bc1_15959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bc1_15959/02_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-5592/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: 7.69, per 1000 atoms: 0.89 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=4, 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 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: 2.37 Conformation dependent library (CDL) restraints added in 934.1 milliseconds 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: 0.56 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: 2.27 Time building geometry restraints manager: 2.72 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: 4742 12.66 - 25.33: 334 25.33 - 37.99: 93 37.99 - 50.65: 31 50.65 - 63.31: 8 Dihedral angle restraints: 5208 sinusoidal: 2094 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 5205 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: 2.03 - 2.60: 88 2.60 - 3.18: 7867 3.18 - 3.75: 14247 3.75 - 4.33: 18388 4.33 - 4.90: 30448 Nonbonded interactions: 71038 Sorted by model distance: nonbonded pdb=" SG CYS B 596 " pdb=" SG CYS B 601 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 331 " pdb=" SG CYS B 372 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS B 338 " pdb=" SG CYS B 365 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS B 349 " pdb=" SG CYS B 807 " model vdw 2.034 3.760 nonbonded pdb=" O LEU B 626 " pdb=" N VAL B 630 " model vdw 2.265 3.120 ... (remaining 71033 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.040 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.460 ------------------------------------------------------------------------------- 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 8928 Z= 0.125 Angle : 0.458 5.542 12130 Z= 0.261 Chirality : 0.036 0.125 1332 Planarity : 0.004 0.032 1486 Dihedral : 10.381 63.314 3196 Min Nonbonded Distance : 2.030 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 *********************** 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 : 0.995 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: 0.9136 time to fit residues: 277.7337 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 : 0.977 ------------------------------------------------------------------------------- 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: 0.7980 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 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 = 0.5247 r_free = 0.5247 target = 0.269674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5051 r_free = 0.5051 target = 0.248620 restraints weight = 14183.017| |-----------------------------------------------------------------------------| r_work (start): 0.5059 rms_B_bonded: 2.60 r_work: 0.4969 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5305 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8928 Z= 0.240 Angle : 0.655 11.445 12130 Z= 0.336 Chirality : 0.042 0.165 1332 Planarity : 0.005 0.045 1486 Dihedral : 4.316 42.878 1172 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.64 % Allowed : 14.56 % Favored : 81.80 % 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 : -0.39 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 408 HIS 0.022 0.003 HIS A 844 PHE 0.014 0.001 PHE B 558 TYR 0.016 0.001 TYR A 668 ARG 0.004 0.001 ARG A 592 *********************** 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 218 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 381 ILE cc_start: 0.6332 (mt) cc_final: 0.6043 (mt) REVERT: A 553 MET cc_start: 0.6829 (tmt) cc_final: 0.6362 (tmm) REVERT: A 595 GLU cc_start: 0.4779 (mp0) cc_final: 0.3304 (tm-30) REVERT: A 613 MET cc_start: 0.7003 (mtp) cc_final: 0.6298 (ttm) REVERT: A 638 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7063 (tmmt) REVERT: A 813 ARG cc_start: 0.4743 (mtt90) cc_final: 0.3254 (ppt170) REVERT: B 294 GLU cc_start: 0.4557 (mm-30) cc_final: 0.4292 (mp0) REVERT: B 381 ILE cc_start: 0.6389 (mt) cc_final: 0.6094 (mt) REVERT: B 553 MET cc_start: 0.6817 (tmt) cc_final: 0.6357 (tmm) REVERT: B 595 GLU cc_start: 0.4373 (mp0) cc_final: 0.3037 (tm-30) REVERT: B 604 GLU cc_start: 0.7508 (tm-30) cc_final: 0.6843 (mt-10) REVERT: B 613 MET cc_start: 0.6996 (mtp) cc_final: 0.6317 (ttm) REVERT: B 638 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7085 (tmmt) REVERT: B 813 ARG cc_start: 0.4800 (mtt90) cc_final: 0.3315 (ppt170) outliers start: 34 outliers final: 8 residues processed: 208 average time/residue: 1.0024 time to fit residues: 224.8288 Evaluate side-chains 147 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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: 5.9990 chunk 74 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.5214 r_free = 0.5214 target = 0.266353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5013 r_free = 0.5013 target = 0.244784 restraints weight = 14268.822| |-----------------------------------------------------------------------------| r_work (start): 0.5025 rms_B_bonded: 2.71 r_work: 0.4930 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5361 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8928 Z= 0.244 Angle : 0.649 9.824 12130 Z= 0.330 Chirality : 0.041 0.152 1332 Planarity : 0.005 0.050 1486 Dihedral : 4.407 41.938 1172 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.18 % Allowed : 17.88 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.35 (0.25), residues: 1026 helix: 1.49 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.61 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 408 HIS 0.012 0.002 HIS A 844 PHE 0.025 0.002 PHE A 558 TYR 0.015 0.001 TYR B 528 ARG 0.009 0.001 ARG B 810 *********************** 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 : 0.959 Fit side-chains REVERT: A 289 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.7078 (tmt90) REVERT: A 294 GLU cc_start: 0.4707 (mm-30) cc_final: 0.4461 (mp0) REVERT: A 381 ILE cc_start: 0.6396 (mt) cc_final: 0.6103 (mt) REVERT: A 553 MET cc_start: 0.6726 (tmt) cc_final: 0.6227 (tmm) REVERT: A 595 GLU cc_start: 0.4970 (mp0) cc_final: 0.3446 (tm-30) REVERT: A 604 GLU cc_start: 0.7562 (tm-30) cc_final: 0.6942 (mt-10) REVERT: A 613 MET cc_start: 0.7059 (mtp) cc_final: 0.6339 (mtp) REVERT: A 638 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7199 (tmmt) REVERT: A 813 ARG cc_start: 0.4770 (mtt90) cc_final: 0.3305 (ppt170) REVERT: B 294 GLU cc_start: 0.4563 (mm-30) cc_final: 0.4188 (mp0) REVERT: B 310 LEU cc_start: 0.5178 (mt) cc_final: 0.4917 (mt) REVERT: B 381 ILE cc_start: 0.6434 (mt) cc_final: 0.6140 (mt) REVERT: B 553 MET cc_start: 0.6751 (tmt) cc_final: 0.6253 (tmm) REVERT: B 592 ARG cc_start: 0.5820 (OUTLIER) cc_final: 0.5406 (mmm-85) REVERT: B 595 GLU cc_start: 0.4238 (mp0) cc_final: 0.3070 (tm-30) REVERT: B 604 GLU cc_start: 0.7536 (tm-30) cc_final: 0.6891 (mt-10) REVERT: B 613 MET cc_start: 0.7066 (mtp) cc_final: 0.6345 (mtp) REVERT: B 638 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7208 (tmmt) REVERT: B 813 ARG cc_start: 0.5017 (mtt90) cc_final: 0.3379 (ppt170) outliers start: 39 outliers final: 15 residues processed: 195 average time/residue: 0.8823 time to fit residues: 187.3880 Evaluate side-chains 163 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 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 668 TYR 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 592 ARG 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: 0.0270 chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 549 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5227 r_free = 0.5227 target = 0.267889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5027 r_free = 0.5027 target = 0.246765 restraints weight = 14242.977| |-----------------------------------------------------------------------------| r_work (start): 0.5023 rms_B_bonded: 2.61 r_work: 0.4927 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5380 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 8928 Z= 0.220 Angle : 0.664 13.449 12130 Z= 0.329 Chirality : 0.041 0.155 1332 Planarity : 0.005 0.050 1486 Dihedral : 4.360 42.350 1170 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.71 % Allowed : 18.09 % 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: 1.28 (0.25), residues: 1026 helix: 1.47 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.71 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 408 HIS 0.007 0.001 HIS A 844 PHE 0.028 0.001 PHE A 558 TYR 0.017 0.001 TYR B 306 ARG 0.007 0.000 ARG A 810 *********************** 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 216 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 294 GLU cc_start: 0.4692 (mm-30) cc_final: 0.4261 (mp0) REVERT: A 381 ILE cc_start: 0.6390 (mt) cc_final: 0.6088 (mt) REVERT: A 553 MET cc_start: 0.6761 (tmt) cc_final: 0.6245 (tmm) REVERT: A 595 GLU cc_start: 0.4842 (mp0) cc_final: 0.3338 (tm-30) REVERT: A 604 GLU cc_start: 0.7496 (tm-30) cc_final: 0.6920 (mt-10) REVERT: A 613 MET cc_start: 0.7053 (mtp) cc_final: 0.6469 (mtp) REVERT: A 638 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7220 (tmmt) REVERT: A 699 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6590 (tp30) REVERT: A 813 ARG cc_start: 0.4784 (mtt90) cc_final: 0.3253 (ppt170) REVERT: B 294 GLU cc_start: 0.4592 (mm-30) cc_final: 0.4146 (mp0) REVERT: B 381 ILE cc_start: 0.6349 (mt) cc_final: 0.6038 (mt) REVERT: B 553 MET cc_start: 0.6807 (tmt) cc_final: 0.6511 (tmt) REVERT: B 595 GLU cc_start: 0.4205 (mp0) cc_final: 0.3017 (tm-30) REVERT: B 604 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7082 (mt-10) REVERT: B 608 GLN cc_start: 0.6145 (tp40) cc_final: 0.5323 (tt0) REVERT: B 613 MET cc_start: 0.7034 (mtp) cc_final: 0.6458 (mtp) REVERT: B 638 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7209 (tmmt) REVERT: B 699 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6706 (tp30) REVERT: B 810 ARG cc_start: 0.0094 (mmp-170) cc_final: -0.0729 (mmp-170) REVERT: B 813 ARG cc_start: 0.5024 (mtt90) cc_final: 0.3383 (ppt170) REVERT: B 857 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7862 (tp) outliers start: 44 outliers final: 16 residues processed: 204 average time/residue: 0.8861 time to fit residues: 196.7650 Evaluate side-chains 174 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 526 THR Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 668 TYR 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 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 699 GLU Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 857 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 64 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 45 optimal weight: 0.0970 chunk 70 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 ASN A 674 GLN B 525 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5184 r_free = 0.5184 target = 0.262691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.239744 restraints weight = 14019.359| |-----------------------------------------------------------------------------| r_work (start): 0.4978 rms_B_bonded: 2.62 r_work: 0.4882 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5521 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 8928 Z= 0.317 Angle : 0.743 12.376 12130 Z= 0.375 Chirality : 0.044 0.147 1332 Planarity : 0.005 0.053 1486 Dihedral : 4.582 37.888 1170 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.60 % Allowed : 19.70 % Favored : 75.70 % 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: 0.89 (0.26), residues: 1026 helix: 1.18 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.87 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 408 HIS 0.004 0.001 HIS A 844 PHE 0.034 0.002 PHE A 558 TYR 0.024 0.002 TYR B 306 ARG 0.008 0.001 ARG A 289 *********************** 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 207 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 0.892 Fit side-chains REVERT: A 553 MET cc_start: 0.6879 (tmt) cc_final: 0.6364 (tmm) REVERT: A 592 ARG cc_start: 0.5811 (OUTLIER) cc_final: 0.5567 (tmm-80) REVERT: A 595 GLU cc_start: 0.4266 (mp0) cc_final: 0.2894 (tm-30) REVERT: A 604 GLU cc_start: 0.7552 (tm-30) cc_final: 0.6837 (mp0) REVERT: A 608 GLN cc_start: 0.6321 (tp40) cc_final: 0.5509 (tt0) REVERT: A 613 MET cc_start: 0.7043 (mtp) cc_final: 0.6494 (mtp) REVERT: A 638 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7115 (tmmt) REVERT: A 699 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7233 (tp30) REVERT: A 813 ARG cc_start: 0.4993 (mtt90) cc_final: 0.3236 (ppt170) REVERT: A 826 ILE cc_start: 0.4585 (OUTLIER) cc_final: 0.4384 (pp) REVERT: B 553 MET cc_start: 0.6929 (tmt) cc_final: 0.6418 (tmm) REVERT: B 595 GLU cc_start: 0.4182 (mp0) cc_final: 0.3090 (tm-30) REVERT: B 604 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7096 (mt-10) REVERT: B 608 GLN cc_start: 0.6298 (tp40) cc_final: 0.5536 (tt0) REVERT: B 613 MET cc_start: 0.7031 (mtp) cc_final: 0.6296 (mtp) REVERT: B 638 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7154 (tmmt) REVERT: B 668 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.7622 (m-10) REVERT: B 699 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7130 (tp30) REVERT: B 810 ARG cc_start: 0.0338 (mmp-170) cc_final: -0.0386 (mtt90) REVERT: B 813 ARG cc_start: 0.5327 (mtt90) cc_final: 0.3552 (ppt170) outliers start: 43 outliers final: 12 residues processed: 190 average time/residue: 0.8593 time to fit residues: 178.1796 Evaluate side-chains 163 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 592 ARG 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 307 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 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 = 0.273363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5030 r_free = 0.5030 target = 0.247667 restraints weight = 13993.101| |-----------------------------------------------------------------------------| r_work (start): 0.4996 rms_B_bonded: 2.85 r_work: 0.4889 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5435 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 8928 Z= 0.263 Angle : 0.754 15.382 12130 Z= 0.372 Chirality : 0.044 0.174 1332 Planarity : 0.005 0.053 1486 Dihedral : 4.484 41.633 1168 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.64 % Allowed : 22.70 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.72 (0.25), residues: 1026 helix: 1.04 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.87 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 408 HIS 0.004 0.001 HIS B 844 PHE 0.032 0.002 PHE A 558 TYR 0.021 0.001 TYR B 306 ARG 0.007 0.001 ARG A 289 *********************** 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 198 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.861 Fit side-chains REVERT: A 530 LYS cc_start: 0.6088 (mmtp) cc_final: 0.5683 (mptm) REVERT: A 534 MET cc_start: 0.6773 (mmt) cc_final: 0.6340 (mmm) REVERT: A 553 MET cc_start: 0.6810 (tmt) cc_final: 0.6294 (tmm) REVERT: A 595 GLU cc_start: 0.4194 (mp0) cc_final: 0.2859 (tm-30) REVERT: A 604 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7100 (mt-10) REVERT: A 608 GLN cc_start: 0.6170 (tp40) cc_final: 0.5386 (tt0) REVERT: A 613 MET cc_start: 0.7049 (mtp) cc_final: 0.6297 (mtp) REVERT: A 638 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7043 (tmmt) REVERT: A 671 MET cc_start: 0.7755 (mmt) cc_final: 0.7310 (mmp) REVERT: A 699 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6432 (tp30) REVERT: A 813 ARG cc_start: 0.4936 (mtt90) cc_final: 0.3161 (ppt170) REVERT: A 826 ILE cc_start: 0.4473 (OUTLIER) cc_final: 0.4222 (pp) REVERT: B 534 MET cc_start: 0.6805 (mmt) cc_final: 0.6583 (mmt) REVERT: B 553 MET cc_start: 0.6824 (tmt) cc_final: 0.6308 (tmm) REVERT: B 592 ARG cc_start: 0.5819 (OUTLIER) cc_final: 0.5408 (tmm-80) REVERT: B 595 GLU cc_start: 0.3727 (mp0) cc_final: 0.2230 (tm-30) REVERT: B 604 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7158 (mt-10) REVERT: B 608 GLN cc_start: 0.6188 (tp40) cc_final: 0.5407 (tt0) REVERT: B 613 MET cc_start: 0.7065 (mtp) cc_final: 0.6296 (mtp) REVERT: B 638 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7025 (tmmt) REVERT: B 699 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6710 (tp30) REVERT: B 718 LYS cc_start: 0.4351 (mmmt) cc_final: 0.3918 (mptt) REVERT: B 810 ARG cc_start: 0.0323 (mmp-170) cc_final: -0.0663 (mtm180) REVERT: B 813 ARG cc_start: 0.5297 (mtt90) cc_final: 0.3382 (ppt170) outliers start: 34 outliers final: 14 residues processed: 186 average time/residue: 0.8840 time to fit residues: 179.5775 Evaluate side-chains 167 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 305 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 VAL 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 592 ARG 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 75 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 45 optimal weight: 0.1980 chunk 6 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN A 674 GLN B 525 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5230 r_free = 0.5230 target = 0.274607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.249075 restraints weight = 14199.035| |-----------------------------------------------------------------------------| r_work (start): 0.5030 rms_B_bonded: 2.89 r_work: 0.4947 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5438 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8928 Z= 0.235 Angle : 0.709 15.994 12130 Z= 0.356 Chirality : 0.043 0.170 1332 Planarity : 0.005 0.057 1486 Dihedral : 4.450 42.285 1168 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.53 % Allowed : 23.66 % Favored : 72.81 % 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: 0.72 (0.25), residues: 1026 helix: 1.05 (0.18), residues: 736 sheet: None (None), residues: 0 loop : -0.90 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 408 HIS 0.003 0.001 HIS B 844 PHE 0.031 0.002 PHE A 558 TYR 0.017 0.001 TYR B 306 ARG 0.009 0.001 ARG A 289 *********************** 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 193 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 530 LYS cc_start: 0.6298 (mmtp) cc_final: 0.5918 (mptm) REVERT: A 534 MET cc_start: 0.6776 (mmt) cc_final: 0.6567 (mmt) REVERT: A 553 MET cc_start: 0.6885 (tmt) cc_final: 0.6357 (tmm) REVERT: A 595 GLU cc_start: 0.3297 (mp0) cc_final: 0.2483 (tm-30) REVERT: A 604 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7107 (mt-10) REVERT: A 608 GLN cc_start: 0.6211 (tp40) cc_final: 0.5413 (tt0) REVERT: A 613 MET cc_start: 0.7027 (mtp) cc_final: 0.6285 (mtp) REVERT: A 638 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7081 (tmmt) REVERT: A 671 MET cc_start: 0.7686 (mmt) cc_final: 0.7339 (mmp) REVERT: A 699 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6155 (tp30) REVERT: A 813 ARG cc_start: 0.4823 (mtt90) cc_final: 0.3083 (ppt170) REVERT: B 530 LYS cc_start: 0.6394 (mmtp) cc_final: 0.6171 (mmtt) REVERT: B 553 MET cc_start: 0.6914 (tmt) cc_final: 0.6388 (tmm) REVERT: B 595 GLU cc_start: 0.3828 (mp0) cc_final: 0.2345 (tm-30) REVERT: B 604 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7158 (mt-10) REVERT: B 608 GLN cc_start: 0.6191 (tp40) cc_final: 0.5404 (tt0) REVERT: B 613 MET cc_start: 0.6981 (mtp) cc_final: 0.6238 (mtp) REVERT: B 638 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7094 (tmmt) REVERT: B 699 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6507 (tp30) REVERT: B 813 ARG cc_start: 0.5257 (mtt90) cc_final: 0.3367 (ppt170) outliers start: 33 outliers final: 15 residues processed: 183 average time/residue: 0.8517 time to fit residues: 170.3878 Evaluate side-chains 163 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 310 LEU 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 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 305 TYR Chi-restraints excluded: chain B residue 307 THR 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 699 GLU Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 805 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 84 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 71 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5227 r_free = 0.5227 target = 0.273400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5042 r_free = 0.5042 target = 0.248718 restraints weight = 14171.993| |-----------------------------------------------------------------------------| r_work (start): 0.5035 rms_B_bonded: 2.82 r_work: 0.4948 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5452 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8928 Z= 0.243 Angle : 0.723 15.873 12130 Z= 0.360 Chirality : 0.043 0.155 1332 Planarity : 0.005 0.056 1486 Dihedral : 4.527 41.169 1168 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.64 % Allowed : 24.84 % Favored : 71.52 % 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: 0.73 (0.26), residues: 1026 helix: 1.08 (0.18), residues: 736 sheet: None (None), residues: 0 loop : -0.94 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 408 HIS 0.002 0.001 HIS A 844 PHE 0.033 0.002 PHE A 558 TYR 0.024 0.001 TYR A 299 ARG 0.005 0.001 ARG A 289 *********************** 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 184 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.969 Fit side-chains REVERT: A 289 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.6433 (ttm-80) REVERT: A 350 PRO cc_start: 0.2734 (Cg_endo) cc_final: 0.2281 (Cg_exo) REVERT: A 530 LYS cc_start: 0.6324 (mmtp) cc_final: 0.5915 (mptm) REVERT: A 534 MET cc_start: 0.6853 (mmt) cc_final: 0.6624 (mmt) REVERT: A 553 MET cc_start: 0.6912 (tmt) cc_final: 0.6383 (tmm) REVERT: A 595 GLU cc_start: 0.3067 (mp0) cc_final: 0.2222 (tm-30) REVERT: A 604 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7030 (mt-10) REVERT: A 608 GLN cc_start: 0.6240 (tp40) cc_final: 0.5448 (tt0) REVERT: A 613 MET cc_start: 0.7045 (mtp) cc_final: 0.6307 (mtp) REVERT: A 638 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7086 (tmmt) REVERT: A 813 ARG cc_start: 0.4863 (mtt90) cc_final: 0.3082 (ppt170) REVERT: A 826 ILE cc_start: 0.4486 (OUTLIER) cc_final: 0.4177 (pp) REVERT: B 553 MET cc_start: 0.6944 (tmt) cc_final: 0.6434 (tmm) REVERT: B 595 GLU cc_start: 0.3349 (mp0) cc_final: 0.2264 (tm-30) REVERT: B 604 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7143 (mp0) REVERT: B 608 GLN cc_start: 0.6261 (tp40) cc_final: 0.5451 (tt0) REVERT: B 613 MET cc_start: 0.7027 (mtp) cc_final: 0.6311 (mtp) REVERT: B 638 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7096 (tmmt) REVERT: B 699 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6711 (tp30) REVERT: B 718 LYS cc_start: 0.4517 (mmmt) cc_final: 0.4052 (mptt) REVERT: B 813 ARG cc_start: 0.5317 (mtt90) cc_final: 0.3428 (ppt170) outliers start: 34 outliers final: 14 residues processed: 173 average time/residue: 0.8347 time to fit residues: 158.3383 Evaluate side-chains 161 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 394 LEU 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 826 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 307 THR 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 601 CYS 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 805 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 59 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5223 r_free = 0.5223 target = 0.273451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5040 r_free = 0.5040 target = 0.248499 restraints weight = 14014.814| |-----------------------------------------------------------------------------| r_work (start): 0.5030 rms_B_bonded: 2.81 r_work: 0.4944 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5468 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8928 Z= 0.250 Angle : 0.729 16.296 12130 Z= 0.364 Chirality : 0.043 0.159 1332 Planarity : 0.005 0.057 1486 Dihedral : 4.587 41.061 1168 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.00 % Allowed : 25.91 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.71 (0.26), residues: 1026 helix: 1.06 (0.18), residues: 736 sheet: None (None), residues: 0 loop : -0.94 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.002 TRP A 408 HIS 0.002 0.000 HIS B 844 PHE 0.035 0.002 PHE A 558 TYR 0.015 0.001 TYR A 528 ARG 0.007 0.001 ARG B 592 *********************** 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 174 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 350 PRO cc_start: 0.2769 (Cg_endo) cc_final: 0.2264 (Cg_exo) REVERT: A 408 TRP cc_start: 0.6635 (m100) cc_final: 0.6426 (m100) REVERT: A 553 MET cc_start: 0.6915 (tmt) cc_final: 0.6389 (tmm) REVERT: A 595 GLU cc_start: 0.3080 (mp0) cc_final: 0.2388 (tm-30) REVERT: A 604 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7025 (mt-10) REVERT: A 608 GLN cc_start: 0.6261 (tp40) cc_final: 0.5458 (tt0) REVERT: A 613 MET cc_start: 0.7024 (mtp) cc_final: 0.6316 (mtp) REVERT: A 638 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7105 (tmmt) REVERT: A 813 ARG cc_start: 0.5178 (mtt90) cc_final: 0.3246 (ppt170) REVERT: A 826 ILE cc_start: 0.4503 (OUTLIER) cc_final: 0.4170 (pp) REVERT: B 289 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.7064 (ttt90) REVERT: B 348 MET cc_start: 0.5019 (mpm) cc_final: 0.4787 (mmm) REVERT: B 553 MET cc_start: 0.6928 (tmt) cc_final: 0.6409 (tmm) REVERT: B 595 GLU cc_start: 0.3474 (mp0) cc_final: 0.2317 (tm-30) REVERT: B 604 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7212 (mp0) REVERT: B 608 GLN cc_start: 0.6235 (tp40) cc_final: 0.5431 (tt0) REVERT: B 613 MET cc_start: 0.7027 (mtp) cc_final: 0.6295 (mtp) REVERT: B 638 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7126 (tmmt) REVERT: B 659 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.6400 (mtp) REVERT: B 699 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6700 (tp30) REVERT: B 714 MET cc_start: 0.6851 (ttm) cc_final: 0.6636 (ttm) REVERT: B 718 LYS cc_start: 0.4599 (mmmt) cc_final: 0.4263 (mptt) REVERT: B 813 ARG cc_start: 0.5225 (mtt90) cc_final: 0.3385 (ppt170) REVERT: B 842 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7214 (mpp) outliers start: 28 outliers final: 18 residues processed: 164 average time/residue: 0.8645 time to fit residues: 155.0646 Evaluate side-chains 168 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 331 CYS 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 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 289 ARG Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 VAL 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 601 CYS Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 659 MET 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 842 MET Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 79 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 63 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.5236 r_free = 0.5236 target = 0.275184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5053 r_free = 0.5053 target = 0.250378 restraints weight = 13948.861| |-----------------------------------------------------------------------------| r_work (start): 0.5046 rms_B_bonded: 2.80 r_work: 0.4965 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5438 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8928 Z= 0.226 Angle : 0.734 16.509 12130 Z= 0.360 Chirality : 0.043 0.167 1332 Planarity : 0.005 0.057 1486 Dihedral : 4.539 42.146 1168 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.89 % Allowed : 26.34 % Favored : 70.77 % 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: 0.74 (0.26), residues: 1026 helix: 1.10 (0.18), residues: 736 sheet: None (None), residues: 0 loop : -0.97 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP A 408 HIS 0.002 0.000 HIS B 844 PHE 0.036 0.002 PHE A 558 TYR 0.017 0.001 TYR A 299 ARG 0.007 0.000 ARG B 592 ********************** 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 173 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: A 408 TRP cc_start: 0.6701 (m100) cc_final: 0.6453 (m100) REVERT: A 468 ILE cc_start: 0.8569 (mm) cc_final: 0.8343 (pt) REVERT: A 530 LYS cc_start: 0.6321 (mmtp) cc_final: 0.6004 (mptm) REVERT: A 534 MET cc_start: 0.6709 (mmt) cc_final: 0.6492 (mmt) REVERT: A 553 MET cc_start: 0.6930 (tmt) cc_final: 0.6416 (tmm) REVERT: A 595 GLU cc_start: 0.3160 (mp0) cc_final: 0.2448 (tm-30) REVERT: A 604 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7157 (mt-10) REVERT: A 608 GLN cc_start: 0.6249 (tp40) cc_final: 0.5419 (tt0) REVERT: A 613 MET cc_start: 0.7080 (mtp) cc_final: 0.6341 (mtp) REVERT: A 638 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7136 (tmmt) REVERT: A 671 MET cc_start: 0.7595 (mmt) cc_final: 0.6975 (mmp) REVERT: A 813 ARG cc_start: 0.5126 (mtt90) cc_final: 0.3214 (ppt170) REVERT: A 826 ILE cc_start: 0.4470 (OUTLIER) cc_final: 0.4152 (pp) REVERT: A 857 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7904 (tp) REVERT: B 348 MET cc_start: 0.5299 (mpm) cc_final: 0.5035 (mmm) REVERT: B 530 LYS cc_start: 0.6296 (mmtt) cc_final: 0.6057 (mptm) REVERT: B 553 MET cc_start: 0.6943 (tmt) cc_final: 0.6430 (tmm) REVERT: B 595 GLU cc_start: 0.3161 (mp0) cc_final: 0.2028 (tm-30) REVERT: B 604 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7211 (mp0) REVERT: B 608 GLN cc_start: 0.6205 (tp40) cc_final: 0.5403 (tt0) REVERT: B 613 MET cc_start: 0.6992 (mtp) cc_final: 0.6269 (mtp) REVERT: B 638 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7203 (tmmt) REVERT: B 699 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6423 (tp30) REVERT: B 718 LYS cc_start: 0.4694 (mmmt) cc_final: 0.4333 (mptt) REVERT: B 810 ARG cc_start: 0.1927 (mmm160) cc_final: 0.1711 (mmm160) REVERT: B 813 ARG cc_start: 0.5190 (mtt90) cc_final: 0.3371 (ppt170) REVERT: B 842 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7239 (mpp) outliers start: 27 outliers final: 16 residues processed: 163 average time/residue: 0.8505 time to fit residues: 151.7169 Evaluate side-chains 162 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 310 LEU Chi-restraints excluded: chain A residue 331 CYS 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 826 ILE Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 VAL 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 601 CYS 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 805 THR 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: 0.0050 chunk 14 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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 = 0.5239 r_free = 0.5239 target = 0.275257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5054 r_free = 0.5054 target = 0.250144 restraints weight = 14105.921| |-----------------------------------------------------------------------------| r_work (start): 0.5040 rms_B_bonded: 2.86 r_work: 0.4956 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5435 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8928 Z= 0.218 Angle : 0.732 16.711 12130 Z= 0.358 Chirality : 0.042 0.175 1332 Planarity : 0.005 0.057 1486 Dihedral : 4.472 41.329 1168 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.89 % Allowed : 26.23 % Favored : 70.88 % 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: 0.76 (0.26), residues: 1026 helix: 1.13 (0.18), residues: 736 sheet: None (None), residues: 0 loop : -1.04 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A 408 HIS 0.002 0.000 HIS B 844 PHE 0.034 0.001 PHE A 558 TYR 0.016 0.001 TYR B 528 ARG 0.007 0.000 ARG B 592 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5323.88 seconds wall clock time: 94 minutes 52.66 seconds (5692.66 seconds total)