Starting phenix.real_space_refine on Sat Dec 28 15:35:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bc1_15959/12_2024/8bc1_15959.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bc1_15959/12_2024/8bc1_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_15959/12_2024/8bc1_15959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bc1_15959/12_2024/8bc1_15959.map" model { file = "/net/cci-nas-00/data/ceres_data/8bc1_15959/12_2024/8bc1_15959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bc1_15959/12_2024/8bc1_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 8.07, per 1000 atoms: 0.93 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: 2.24 Conformation dependent library (CDL) restraints added in 981.3 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: 0.77 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: 2.26 Time building geometry restraints manager: 2.53 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: 0.00 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: 0.900 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.630 Find NCS groups from input model: 0.260 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:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 39.470 ------------------------------------------------------------------------------- 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 : 0.981 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: 0.9143 time to fit residues: 277.6539 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 : 0.966 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5351 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 : 1.006 Fit side-chains revert: symmetry clash REVERT: A 381 ILE cc_start: 0.6077 (mt) cc_final: 0.5798 (mt) REVERT: A 553 MET cc_start: 0.6691 (tmt) cc_final: 0.6212 (tmm) REVERT: A 595 GLU cc_start: 0.4852 (mp0) cc_final: 0.3346 (tm-30) REVERT: A 613 MET cc_start: 0.6987 (mtp) cc_final: 0.6186 (ttm) REVERT: A 638 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.6962 (tmmt) REVERT: A 813 ARG cc_start: 0.4603 (mtt90) cc_final: 0.3232 (ppt170) REVERT: B 294 GLU cc_start: 0.4839 (mm-30) cc_final: 0.4450 (mp0) REVERT: B 381 ILE cc_start: 0.6071 (mt) cc_final: 0.5786 (mt) REVERT: B 386 MET cc_start: 0.5010 (mmp) cc_final: 0.4791 (mmm) REVERT: B 553 MET cc_start: 0.6677 (tmt) cc_final: 0.6197 (tmm) REVERT: B 595 GLU cc_start: 0.4482 (mp0) cc_final: 0.3080 (tm-30) REVERT: B 604 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6953 (mt-10) REVERT: B 613 MET cc_start: 0.6989 (mtp) cc_final: 0.6202 (ttm) REVERT: B 638 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.6963 (tmmt) REVERT: B 813 ARG cc_start: 0.4661 (mtt90) cc_final: 0.3287 (ppt170) outliers start: 34 outliers final: 8 residues processed: 208 average time/residue: 1.0420 time to fit residues: 233.5848 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 : 1.081 ------------------------------------------------------------------------------- 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 52 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 93 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5388 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8928 Z= 0.233 Angle : 0.643 9.881 12130 Z= 0.325 Chirality : 0.041 0.152 1332 Planarity : 0.005 0.049 1486 Dihedral : 4.387 42.542 1172 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.07 % Allowed : 17.77 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.40 (0.25), residues: 1026 helix: 1.52 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.57 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 408 HIS 0.012 0.002 HIS A 844 PHE 0.024 0.001 PHE A 558 TYR 0.015 0.001 TYR B 528 ARG 0.024 0.001 ARG A 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 206 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 0.937 Fit side-chains REVERT: A 289 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6903 (tmt90) REVERT: A 294 GLU cc_start: 0.4798 (mm-30) cc_final: 0.4482 (mp0) REVERT: A 381 ILE cc_start: 0.6022 (mt) cc_final: 0.5729 (mt) REVERT: A 553 MET cc_start: 0.6651 (tmt) cc_final: 0.6126 (tmm) REVERT: A 595 GLU cc_start: 0.5120 (mp0) cc_final: 0.3562 (tm-30) REVERT: A 604 GLU cc_start: 0.7289 (tm-30) cc_final: 0.6982 (mt-10) REVERT: A 613 MET cc_start: 0.7141 (mtp) cc_final: 0.6636 (mtp) REVERT: A 638 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7171 (tmmt) REVERT: A 813 ARG cc_start: 0.4551 (mtt90) cc_final: 0.3238 (ppt170) REVERT: B 294 GLU cc_start: 0.4805 (mm-30) cc_final: 0.4310 (mp0) REVERT: B 381 ILE cc_start: 0.6017 (mt) cc_final: 0.5727 (mt) REVERT: B 386 MET cc_start: 0.5474 (mmp) cc_final: 0.5260 (mmm) REVERT: B 553 MET cc_start: 0.6668 (tmt) cc_final: 0.6157 (tmm) REVERT: B 592 ARG cc_start: 0.5743 (OUTLIER) cc_final: 0.5349 (mmm-85) REVERT: B 595 GLU cc_start: 0.4395 (mp0) cc_final: 0.3298 (tm-30) REVERT: B 604 GLU cc_start: 0.7214 (tm-30) cc_final: 0.6988 (mt-10) REVERT: B 613 MET cc_start: 0.7143 (mtp) cc_final: 0.6525 (mtp) REVERT: B 638 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7173 (tmmt) REVERT: B 813 ARG cc_start: 0.4662 (mtt90) cc_final: 0.3301 (ppt170) outliers start: 38 outliers final: 15 residues processed: 192 average time/residue: 0.9363 time to fit residues: 195.0625 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 : 1.019 ------------------------------------------------------------------------------- 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 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 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 93 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 45 optimal weight: 0.1980 chunk 63 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5381 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8928 Z= 0.207 Angle : 0.650 13.342 12130 Z= 0.320 Chirality : 0.041 0.141 1332 Planarity : 0.005 0.049 1486 Dihedral : 4.365 42.833 1172 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.93 % Allowed : 17.99 % Favored : 77.09 % 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: 1.29 (0.25), residues: 1026 helix: 1.46 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.64 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 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 A 528 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 214 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 1.138 Fit side-chains REVERT: A 294 GLU cc_start: 0.4841 (mm-30) cc_final: 0.4319 (mp0) REVERT: A 348 MET cc_start: 0.6272 (OUTLIER) cc_final: 0.6064 (mpm) REVERT: A 381 ILE cc_start: 0.6042 (mt) cc_final: 0.5752 (mt) REVERT: A 408 TRP cc_start: 0.6895 (m-10) cc_final: 0.6605 (m-10) REVERT: A 553 MET cc_start: 0.6638 (tmt) cc_final: 0.6112 (tmm) REVERT: A 595 GLU cc_start: 0.5029 (mp0) cc_final: 0.3533 (tm-30) REVERT: A 604 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6777 (mp0) REVERT: A 613 MET cc_start: 0.7149 (mtp) cc_final: 0.6612 (mtp) REVERT: A 638 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7160 (tmmt) REVERT: A 699 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6821 (tp30) REVERT: A 813 ARG cc_start: 0.4576 (mtt90) cc_final: 0.3192 (ppt170) REVERT: B 294 GLU cc_start: 0.4907 (mm-30) cc_final: 0.4313 (mp0) REVERT: B 381 ILE cc_start: 0.6028 (mt) cc_final: 0.5725 (mt) REVERT: B 386 MET cc_start: 0.5486 (mmp) cc_final: 0.5113 (mmm) REVERT: B 408 TRP cc_start: 0.6797 (m-10) cc_final: 0.6523 (m-10) REVERT: B 553 MET cc_start: 0.6627 (tmt) cc_final: 0.6316 (tmt) REVERT: B 595 GLU cc_start: 0.4721 (mp0) cc_final: 0.3267 (tm-30) REVERT: B 613 MET cc_start: 0.7144 (mtp) cc_final: 0.6605 (mtp) REVERT: B 638 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7163 (tmmt) REVERT: B 810 ARG cc_start: 0.0443 (mmp-170) cc_final: 0.0204 (mpp-170) REVERT: B 813 ARG cc_start: 0.4819 (mtt90) cc_final: 0.3348 (ppt170) REVERT: B 857 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8003 (tp) outliers start: 46 outliers final: 12 residues processed: 200 average time/residue: 0.9138 time to fit residues: 198.4529 Evaluate side-chains 168 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 57 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 GLN B 525 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5412 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 8928 Z= 0.223 Angle : 0.670 13.210 12130 Z= 0.329 Chirality : 0.041 0.147 1332 Planarity : 0.005 0.052 1486 Dihedral : 4.315 41.322 1170 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.96 % Allowed : 19.91 % Favored : 76.12 % 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: 1.48 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.72 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 408 HIS 0.005 0.001 HIS A 844 PHE 0.030 0.002 PHE A 558 TYR 0.017 0.001 TYR A 528 ARG 0.004 0.000 ARG A 542 *********************** 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 203 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.974 Fit side-chains REVERT: A 294 GLU cc_start: 0.4960 (mm-30) cc_final: 0.4359 (mp0) REVERT: A 381 ILE cc_start: 0.5994 (mt) cc_final: 0.5725 (mt) REVERT: A 408 TRP cc_start: 0.6997 (m-10) cc_final: 0.6629 (m-10) REVERT: A 534 MET cc_start: 0.6806 (mmt) cc_final: 0.6589 (mmt) REVERT: A 553 MET cc_start: 0.6656 (tmt) cc_final: 0.6330 (tmt) REVERT: A 592 ARG cc_start: 0.5505 (OUTLIER) cc_final: 0.5287 (tmm-80) REVERT: A 595 GLU cc_start: 0.4337 (mp0) cc_final: 0.2883 (tm-30) REVERT: A 604 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6959 (mt-10) REVERT: A 613 MET cc_start: 0.7135 (mtp) cc_final: 0.6643 (mtp) REVERT: A 638 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7126 (tmmt) REVERT: A 699 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6911 (tp30) REVERT: A 813 ARG cc_start: 0.4687 (mtt90) cc_final: 0.3191 (ppt170) REVERT: B 294 GLU cc_start: 0.4953 (mm-30) cc_final: 0.4352 (mp0) REVERT: B 381 ILE cc_start: 0.5982 (mt) cc_final: 0.5706 (mt) REVERT: B 386 MET cc_start: 0.5620 (mmp) cc_final: 0.5240 (mmm) REVERT: B 408 TRP cc_start: 0.6915 (m-10) cc_final: 0.6709 (m-10) REVERT: B 534 MET cc_start: 0.6839 (mmt) cc_final: 0.6622 (mmt) REVERT: B 553 MET cc_start: 0.6652 (tmt) cc_final: 0.6122 (tmm) REVERT: B 595 GLU cc_start: 0.4600 (mp0) cc_final: 0.3240 (tm-30) REVERT: B 604 GLU cc_start: 0.6122 (mt-10) cc_final: 0.5901 (pm20) REVERT: B 611 ILE cc_start: 0.7643 (mm) cc_final: 0.7434 (mm) REVERT: B 613 MET cc_start: 0.7225 (mtp) cc_final: 0.6709 (mtp) REVERT: B 638 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7157 (tmmt) REVERT: B 810 ARG cc_start: 0.1037 (mmp-170) cc_final: 0.0319 (mpp-170) REVERT: B 813 ARG cc_start: 0.4952 (mtt90) cc_final: 0.3376 (ppt170) outliers start: 37 outliers final: 15 residues processed: 188 average time/residue: 0.9254 time to fit residues: 189.0830 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 : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 805 THR Chi-restraints excluded: chain A residue 826 ILE 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 738 VAL Chi-restraints excluded: chain B residue 805 THR 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 90 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 ASN B 328 GLN B 549 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5456 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 8928 Z= 0.252 Angle : 0.699 14.871 12130 Z= 0.346 Chirality : 0.043 0.193 1332 Planarity : 0.005 0.054 1486 Dihedral : 4.427 40.589 1170 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.96 % Allowed : 20.45 % Favored : 75.59 % 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: 1.09 (0.25), residues: 1026 helix: 1.34 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.84 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 829 HIS 0.004 0.001 HIS B 844 PHE 0.035 0.002 PHE A 558 TYR 0.017 0.001 TYR A 528 ARG 0.006 0.001 ARG B 542 *********************** 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: 37 poor density : 161 time to evaluate : 1.003 Fit side-chains REVERT: A 294 GLU cc_start: 0.4977 (mm-30) cc_final: 0.4426 (mp0) REVERT: A 381 ILE cc_start: 0.6170 (mt) cc_final: 0.5891 (mt) REVERT: A 408 TRP cc_start: 0.7071 (m-10) cc_final: 0.6767 (m-10) REVERT: A 553 MET cc_start: 0.6681 (tmt) cc_final: 0.6154 (tmm) REVERT: A 595 GLU cc_start: 0.4214 (mp0) cc_final: 0.2801 (tm-30) REVERT: A 604 GLU cc_start: 0.7192 (tm-30) cc_final: 0.6943 (mt-10) REVERT: A 611 ILE cc_start: 0.7651 (mm) cc_final: 0.7450 (mm) REVERT: A 613 MET cc_start: 0.6987 (mtp) cc_final: 0.6499 (mtp) REVERT: A 638 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7071 (tmmt) REVERT: A 699 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7120 (tp30) REVERT: A 813 ARG cc_start: 0.4814 (mtt90) cc_final: 0.3142 (ppt170) REVERT: B 294 GLU cc_start: 0.5055 (mm-30) cc_final: 0.4407 (mp0) REVERT: B 381 ILE cc_start: 0.6155 (mt) cc_final: 0.5875 (mt) REVERT: B 386 MET cc_start: 0.5483 (mmp) cc_final: 0.5157 (mmm) REVERT: B 408 TRP cc_start: 0.7061 (m-10) cc_final: 0.6619 (m100) REVERT: B 553 MET cc_start: 0.6695 (tmt) cc_final: 0.6141 (tmm) REVERT: B 595 GLU cc_start: 0.4413 (mp0) cc_final: 0.2930 (tm-30) REVERT: B 604 GLU cc_start: 0.6265 (mt-10) cc_final: 0.6053 (pm20) REVERT: B 608 GLN cc_start: 0.6240 (tp40) cc_final: 0.5514 (tt0) REVERT: B 611 ILE cc_start: 0.7677 (mm) cc_final: 0.7462 (mm) REVERT: B 613 MET cc_start: 0.6906 (mtp) cc_final: 0.6242 (mtp) REVERT: B 638 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7156 (tmmt) REVERT: B 668 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.7488 (m-10) REVERT: B 810 ARG cc_start: 0.0194 (mmp-170) cc_final: -0.0254 (mtm110) REVERT: B 813 ARG cc_start: 0.5222 (mtt90) cc_final: 0.3527 (ppt170) outliers start: 37 outliers final: 15 residues processed: 183 average time/residue: 0.8973 time to fit residues: 178.5369 Evaluate side-chains 167 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 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 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 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 11 optimal weight: 0.2980 chunk 57 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 0.3980 chunk 100 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 0.0040 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5431 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8928 Z= 0.228 Angle : 0.703 15.798 12130 Z= 0.349 Chirality : 0.043 0.366 1332 Planarity : 0.005 0.054 1486 Dihedral : 4.436 42.272 1168 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.32 % Allowed : 22.27 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.25), residues: 1026 helix: 1.35 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.82 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 829 HIS 0.003 0.001 HIS B 844 PHE 0.032 0.002 PHE A 558 TYR 0.017 0.001 TYR A 528 ARG 0.005 0.000 ARG B 420 *********************** 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 186 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.989 Fit side-chains REVERT: A 294 GLU cc_start: 0.5253 (mm-30) cc_final: 0.4633 (mp0) REVERT: A 381 ILE cc_start: 0.6119 (mt) cc_final: 0.5877 (mt) REVERT: A 408 TRP cc_start: 0.7026 (m-10) cc_final: 0.6724 (m-10) REVERT: A 553 MET cc_start: 0.6697 (tmt) cc_final: 0.6164 (tmm) REVERT: A 595 GLU cc_start: 0.3496 (mp0) cc_final: 0.2504 (tm-30) REVERT: A 604 GLU cc_start: 0.7203 (tm-30) cc_final: 0.6926 (mt-10) REVERT: A 611 ILE cc_start: 0.7616 (mm) cc_final: 0.7408 (mm) REVERT: A 613 MET cc_start: 0.6850 (mtp) cc_final: 0.6206 (mtp) REVERT: A 638 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7143 (tmmt) REVERT: A 699 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6732 (tp30) REVERT: A 813 ARG cc_start: 0.4773 (mtt90) cc_final: 0.3100 (ppt170) REVERT: A 842 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7289 (mpp) REVERT: B 294 GLU cc_start: 0.5247 (mm-30) cc_final: 0.4590 (mp0) REVERT: B 381 ILE cc_start: 0.5982 (mt) cc_final: 0.5740 (mt) REVERT: B 386 MET cc_start: 0.5294 (mmp) cc_final: 0.4961 (mmm) REVERT: B 408 TRP cc_start: 0.7003 (m-10) cc_final: 0.6603 (m100) REVERT: B 530 LYS cc_start: 0.6237 (mmtp) cc_final: 0.6002 (mmtt) REVERT: B 553 MET cc_start: 0.6698 (tmt) cc_final: 0.6146 (tmm) REVERT: B 592 ARG cc_start: 0.5503 (OUTLIER) cc_final: 0.4799 (tmm-80) REVERT: B 595 GLU cc_start: 0.3846 (mp0) cc_final: 0.2432 (tm-30) REVERT: B 611 ILE cc_start: 0.7638 (mm) cc_final: 0.7419 (mm) REVERT: B 613 MET cc_start: 0.6849 (mtp) cc_final: 0.6205 (mtp) REVERT: B 638 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7144 (tmmt) REVERT: B 810 ARG cc_start: 0.0854 (mmp-170) cc_final: 0.0004 (mpp-170) REVERT: B 813 ARG cc_start: 0.5125 (mtt90) cc_final: 0.3429 (ppt170) REVERT: B 842 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7257 (mpp) outliers start: 31 outliers final: 15 residues processed: 176 average time/residue: 0.9452 time to fit residues: 180.5441 Evaluate side-chains 167 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 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 A residue 842 MET 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 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 805 THR Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5474 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8928 Z= 0.242 Angle : 0.718 15.783 12130 Z= 0.356 Chirality : 0.043 0.215 1332 Planarity : 0.005 0.056 1486 Dihedral : 4.537 45.292 1168 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.89 % Allowed : 23.02 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.25), residues: 1026 helix: 1.19 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.91 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 829 HIS 0.002 0.001 HIS A 844 PHE 0.034 0.002 PHE A 558 TYR 0.019 0.001 TYR A 528 ARG 0.006 0.001 ARG B 542 *********************** 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 173 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 1.127 Fit side-chains REVERT: A 553 MET cc_start: 0.6749 (tmt) cc_final: 0.6215 (tmm) REVERT: A 595 GLU cc_start: 0.3482 (mp0) cc_final: 0.2410 (tm-30) REVERT: A 604 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6812 (mt-10) REVERT: A 611 ILE cc_start: 0.7640 (mm) cc_final: 0.7425 (mm) REVERT: A 613 MET cc_start: 0.6951 (mtp) cc_final: 0.6329 (mtp) REVERT: A 638 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7061 (tmmt) REVERT: A 671 MET cc_start: 0.7550 (mmt) cc_final: 0.7075 (mmt) REVERT: A 699 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6399 (tp30) REVERT: A 813 ARG cc_start: 0.4753 (mtt90) cc_final: 0.3157 (ppt170) REVERT: A 842 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7279 (mpp) REVERT: B 294 GLU cc_start: 0.5596 (mm-30) cc_final: 0.4509 (mp0) REVERT: B 381 ILE cc_start: 0.6122 (mt) cc_final: 0.5877 (mt) REVERT: B 386 MET cc_start: 0.5460 (mmp) cc_final: 0.5147 (mmm) REVERT: B 553 MET cc_start: 0.6737 (tmt) cc_final: 0.6205 (tmm) REVERT: B 555 MET cc_start: 0.7536 (mmm) cc_final: 0.7117 (tpt) REVERT: B 595 GLU cc_start: 0.3809 (mp0) cc_final: 0.2586 (tm-30) REVERT: B 608 GLN cc_start: 0.6227 (tp40) cc_final: 0.5538 (tt0) REVERT: B 611 ILE cc_start: 0.7655 (mm) cc_final: 0.7424 (mm) REVERT: B 613 MET cc_start: 0.6928 (mtp) cc_final: 0.6455 (mtp) REVERT: B 638 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7146 (tmmt) REVERT: B 668 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.7579 (m-10) REVERT: B 671 MET cc_start: 0.7604 (mmt) cc_final: 0.7343 (mmp) REVERT: B 699 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6218 (tp30) REVERT: B 810 ARG cc_start: 0.0252 (mmp-170) cc_final: -0.0603 (mmp-170) REVERT: B 813 ARG cc_start: 0.5311 (mtt90) cc_final: 0.3526 (ppt170) REVERT: B 842 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7258 (mpp) outliers start: 27 outliers final: 14 residues processed: 163 average time/residue: 0.9914 time to fit residues: 175.3604 Evaluate side-chains 164 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 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 A residue 842 MET 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 805 THR Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5477 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8928 Z= 0.245 Angle : 0.728 16.734 12130 Z= 0.360 Chirality : 0.043 0.231 1332 Planarity : 0.005 0.056 1486 Dihedral : 4.514 41.164 1168 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.32 % Allowed : 23.23 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 1.13 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.91 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 408 HIS 0.002 0.001 HIS A 844 PHE 0.036 0.002 PHE A 558 TYR 0.015 0.001 TYR A 528 ARG 0.011 0.001 ARG A 289 *********************** 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 179 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 1.107 Fit side-chains REVERT: A 530 LYS cc_start: 0.6220 (mmtt) cc_final: 0.6009 (mmtt) REVERT: A 553 MET cc_start: 0.6748 (tmt) cc_final: 0.6211 (tmm) REVERT: A 595 GLU cc_start: 0.3488 (mp0) cc_final: 0.2414 (tm-30) REVERT: A 604 GLU cc_start: 0.7163 (tm-30) cc_final: 0.6814 (mt-10) REVERT: A 608 GLN cc_start: 0.6245 (tp40) cc_final: 0.5515 (tt0) REVERT: A 611 ILE cc_start: 0.7582 (mm) cc_final: 0.7379 (mm) REVERT: A 613 MET cc_start: 0.6976 (mtp) cc_final: 0.6347 (mtp) REVERT: A 638 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7080 (tmmt) REVERT: A 813 ARG cc_start: 0.5021 (mtt90) cc_final: 0.3210 (ppt170) REVERT: A 842 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7246 (mpp) REVERT: B 289 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6924 (tmt90) REVERT: B 381 ILE cc_start: 0.6113 (mt) cc_final: 0.5902 (mt) REVERT: B 386 MET cc_start: 0.5481 (mmp) cc_final: 0.5200 (mmm) REVERT: B 468 ILE cc_start: 0.8695 (mm) cc_final: 0.8486 (pt) REVERT: B 530 LYS cc_start: 0.6172 (mmtt) cc_final: 0.5850 (mmtt) REVERT: B 534 MET cc_start: 0.6823 (mmt) cc_final: 0.6584 (mmt) REVERT: B 553 MET cc_start: 0.6736 (tmt) cc_final: 0.6205 (tmm) REVERT: B 555 MET cc_start: 0.7486 (mmm) cc_final: 0.7009 (tpt) REVERT: B 595 GLU cc_start: 0.3846 (mp0) cc_final: 0.2679 (tm-30) REVERT: B 608 GLN cc_start: 0.6230 (tp40) cc_final: 0.5574 (tt0) REVERT: B 611 ILE cc_start: 0.7657 (mm) cc_final: 0.7421 (mm) REVERT: B 613 MET cc_start: 0.6968 (mtp) cc_final: 0.6497 (mtp) REVERT: B 638 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7130 (tmmt) REVERT: B 813 ARG cc_start: 0.5476 (mtt90) cc_final: 0.3609 (ppt170) REVERT: B 842 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7265 (mpp) outliers start: 31 outliers final: 16 residues processed: 167 average time/residue: 0.9676 time to fit residues: 175.2410 Evaluate side-chains 164 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 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 738 VAL Chi-restraints excluded: chain A residue 826 ILE 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 467 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 638 LYS 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 46 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 63 optimal weight: 0.0970 chunk 50 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5459 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8928 Z= 0.233 Angle : 0.731 16.991 12130 Z= 0.363 Chirality : 0.043 0.215 1332 Planarity : 0.005 0.057 1486 Dihedral : 4.529 41.503 1168 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.78 % Allowed : 24.73 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 1.11 (0.18), residues: 738 sheet: None (None), residues: 0 loop : -0.95 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 408 HIS 0.002 0.000 HIS A 844 PHE 0.035 0.002 PHE A 558 TYR 0.016 0.001 TYR A 528 ARG 0.005 0.001 ARG A 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: 26 poor density : 147 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: A 468 ILE cc_start: 0.8653 (mm) cc_final: 0.8424 (pt) REVERT: A 530 LYS cc_start: 0.6108 (mmtt) cc_final: 0.5897 (mmtt) REVERT: A 553 MET cc_start: 0.6739 (tmt) cc_final: 0.6209 (tmm) REVERT: A 595 GLU cc_start: 0.3503 (mp0) cc_final: 0.2428 (tm-30) REVERT: A 604 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6789 (mt-10) REVERT: A 608 GLN cc_start: 0.6212 (tp40) cc_final: 0.5506 (tt0) REVERT: A 611 ILE cc_start: 0.7534 (mm) cc_final: 0.7318 (mm) REVERT: A 613 MET cc_start: 0.6944 (mtp) cc_final: 0.6310 (mtp) REVERT: A 638 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7071 (tmmt) REVERT: A 813 ARG cc_start: 0.5082 (mtt90) cc_final: 0.3306 (ppt170) REVERT: A 842 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7211 (mpp) REVERT: A 857 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.8026 (tp) REVERT: B 386 MET cc_start: 0.5415 (mmp) cc_final: 0.5180 (mmm) REVERT: B 468 ILE cc_start: 0.8742 (mm) cc_final: 0.8541 (pt) REVERT: B 530 LYS cc_start: 0.6314 (mmtt) cc_final: 0.5976 (mmtt) REVERT: B 534 MET cc_start: 0.6836 (mmt) cc_final: 0.6613 (mmt) REVERT: B 553 MET cc_start: 0.6732 (tmt) cc_final: 0.6208 (tmm) REVERT: B 595 GLU cc_start: 0.3787 (mp0) cc_final: 0.2660 (tm-30) REVERT: B 608 GLN cc_start: 0.6217 (tp40) cc_final: 0.5531 (tt0) REVERT: B 611 ILE cc_start: 0.7634 (mm) cc_final: 0.7390 (mm) REVERT: B 613 MET cc_start: 0.6912 (mtp) cc_final: 0.6444 (mtp) REVERT: B 638 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7150 (tmmt) REVERT: B 813 ARG cc_start: 0.5508 (mtt90) cc_final: 0.3611 (ppt170) REVERT: B 842 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7237 (mpp) outliers start: 26 outliers final: 16 residues processed: 164 average time/residue: 0.9082 time to fit residues: 162.2931 Evaluate side-chains 164 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 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 738 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 286 ASP 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 467 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 638 LYS 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 76 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 34 optimal weight: 0.0470 chunk 84 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 72 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.273956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5060 r_free = 0.5060 target = 0.250731 restraints weight = 14231.586| |-----------------------------------------------------------------------------| r_work (start): 0.5048 rms_B_bonded: 2.77 r_work: 0.4958 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5422 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8928 Z= 0.220 Angle : 0.722 17.059 12130 Z= 0.357 Chirality : 0.043 0.211 1332 Planarity : 0.005 0.057 1486 Dihedral : 4.495 41.661 1168 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.36 % Allowed : 25.48 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.77 (0.26), residues: 1026 helix: 1.11 (0.18), residues: 738 sheet: None (None), residues: 0 loop : -0.96 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 408 HIS 0.002 0.000 HIS A 844 PHE 0.036 0.001 PHE A 558 TYR 0.016 0.001 TYR A 528 ARG 0.005 0.001 ARG B 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3471.39 seconds wall clock time: 62 minutes 55.65 seconds (3775.65 seconds total)