Starting phenix.real_space_refine on Tue Feb 11 16:43:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7to0_26025/02_2025/7to0_26025.cif Found real_map, /net/cci-nas-00/data/ceres_data/7to0_26025/02_2025/7to0_26025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7to0_26025/02_2025/7to0_26025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7to0_26025/02_2025/7to0_26025.map" model { file = "/net/cci-nas-00/data/ceres_data/7to0_26025/02_2025/7to0_26025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7to0_26025/02_2025/7to0_26025.cif" } resolution = 3.5 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= -0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 23 5.49 5 S 33 5.16 5 C 3727 2.51 5 N 1027 2.21 5 O 1178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 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: 5989 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5479 Classifications: {'peptide': 682} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 653} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 256 Classifications: {'RNA': 12} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna3p': 11} Chain: "C" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 253 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 7} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4555 SG CYS A 810 22.813 42.767 28.664 1.00 39.79 S ATOM 4994 SG CYS A 864 21.545 40.805 25.017 1.00 55.33 S ATOM 5033 SG CYS A 869 23.244 44.391 24.842 1.00 53.89 S Time building chain proxies: 4.22, per 1000 atoms: 0.70 Number of scatterers: 5989 At special positions: 0 Unit cell: (97.188, 85.44, 77.964, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 33 16.00 P 23 15.00 O 1178 8.00 N 1027 7.00 C 3727 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 904.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1300 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 6 sheets defined 47.5% alpha, 6.9% beta 9 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'A' and resid 244 through 252 removed outlier: 3.693A pdb=" N LEU A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 282 removed outlier: 4.041A pdb=" N LYS A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 333 through 340 Processing helix chain 'A' and resid 347 through 358 removed outlier: 3.603A pdb=" N GLY A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 377 Processing helix chain 'A' and resid 381 through 396 Processing helix chain 'A' and resid 419 through 434 removed outlier: 3.697A pdb=" N ASP A 425 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 469 through 488 removed outlier: 3.909A pdb=" N TYR A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE A 474 " --> pdb=" O LYS A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 removed outlier: 4.150A pdb=" N SER A 497 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 521 removed outlier: 3.626A pdb=" N VAL A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 558 removed outlier: 3.591A pdb=" N HIS A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 576 Processing helix chain 'A' and resid 580 through 603 removed outlier: 3.689A pdb=" N ASP A 585 " --> pdb=" O GLU A 581 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP A 603 " --> pdb=" O SER A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 636 through 649 removed outlier: 3.783A pdb=" N ASP A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 684 removed outlier: 3.631A pdb=" N ILE A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 701 Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 744 through 769 removed outlier: 3.760A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 794 Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 296 Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 460 removed outlier: 6.842A pdb=" N GLN A 457 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU A 740 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE A 459 " --> pdb=" O LEU A 740 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819 removed outlier: 7.293A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 831 through 832 Processing sheet with id=AA6, first strand: chain 'A' and resid 842 through 846 removed outlier: 6.652A pdb=" N LYS A 858 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LYS A 878 " --> pdb=" O LYS A 858 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 862 " --> pdb=" O GLY A 874 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY A 874 " --> pdb=" O ILE A 862 " (cutoff:3.500A) 243 hydrogen bonds defined for protein. 708 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1640 1.33 - 1.45: 1039 1.45 - 1.58: 3388 1.58 - 1.70: 45 1.70 - 1.82: 46 Bond restraints: 6158 Sorted by residual: bond pdb=" N VAL A 452 " pdb=" CA VAL A 452 " ideal model delta sigma weight residual 1.459 1.494 -0.035 9.10e-03 1.21e+04 1.51e+01 bond pdb=" CA SER A 891 " pdb=" CB SER A 891 " ideal model delta sigma weight residual 1.524 1.486 0.037 1.31e-02 5.83e+03 8.09e+00 bond pdb=" N ILE A 489 " pdb=" CA ILE A 489 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.22e-02 6.72e+03 8.02e+00 bond pdb=" N ILE A 262 " pdb=" CA ILE A 262 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.95e+00 bond pdb=" N VAL A 414 " pdb=" CA VAL A 414 " ideal model delta sigma weight residual 1.452 1.485 -0.033 1.18e-02 7.18e+03 7.89e+00 ... (remaining 6153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 7073 1.69 - 3.38: 1308 3.38 - 5.07: 36 5.07 - 6.77: 3 6.77 - 8.46: 1 Bond angle restraints: 8421 Sorted by residual: angle pdb=" C THR A 347 " pdb=" N PRO A 348 " pdb=" CA PRO A 348 " ideal model delta sigma weight residual 119.47 127.93 -8.46 1.16e+00 7.43e-01 5.32e+01 angle pdb=" N VAL A 414 " pdb=" CA VAL A 414 " pdb=" C VAL A 414 " ideal model delta sigma weight residual 112.96 107.77 5.19 1.00e+00 1.00e+00 2.69e+01 angle pdb=" N ARG A 316 " pdb=" CA ARG A 316 " pdb=" C ARG A 316 " ideal model delta sigma weight residual 114.75 109.47 5.28 1.26e+00 6.30e-01 1.75e+01 angle pdb=" C THR A 347 " pdb=" CA THR A 347 " pdb=" CB THR A 347 " ideal model delta sigma weight residual 109.31 113.67 -4.36 1.23e+00 6.61e-01 1.26e+01 angle pdb=" N THR A 347 " pdb=" CA THR A 347 " pdb=" C THR A 347 " ideal model delta sigma weight residual 109.62 104.76 4.86 1.45e+00 4.76e-01 1.13e+01 ... (remaining 8416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 3347 17.65 - 35.30: 309 35.30 - 52.95: 94 52.95 - 70.60: 35 70.60 - 88.25: 14 Dihedral angle restraints: 3799 sinusoidal: 1797 harmonic: 2002 Sorted by residual: dihedral pdb=" O4' G B 12 " pdb=" C1' G B 12 " pdb=" N9 G B 12 " pdb=" C4 G B 12 " ideal model delta sinusoidal sigma weight residual -106.00 -155.28 49.28 1 1.70e+01 3.46e-03 1.15e+01 dihedral pdb=" CA GLY A 659 " pdb=" C GLY A 659 " pdb=" N ILE A 660 " pdb=" CA ILE A 660 " ideal model delta harmonic sigma weight residual -180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ASP A 822 " pdb=" CB ASP A 822 " pdb=" CG ASP A 822 " pdb=" OD1 ASP A 822 " ideal model delta sinusoidal sigma weight residual -30.00 -85.56 55.56 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 3796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 543 0.058 - 0.116: 327 0.116 - 0.174: 84 0.174 - 0.232: 1 0.232 - 0.290: 1 Chirality restraints: 956 Sorted by residual: chirality pdb=" CB VAL A 442 " pdb=" CA VAL A 442 " pdb=" CG1 VAL A 442 " pdb=" CG2 VAL A 442 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CB VAL A 453 " pdb=" CA VAL A 453 " pdb=" CG1 VAL A 453 " pdb=" CG2 VAL A 453 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE A 780 " pdb=" CA ILE A 780 " pdb=" CG1 ILE A 780 " pdb=" CG2 ILE A 780 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 953 not shown) Planarity restraints: 994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 9 " -0.025 2.00e-02 2.50e+03 1.30e-02 5.09e+00 pdb=" N9 G B 9 " 0.025 2.00e-02 2.50e+03 pdb=" C8 G B 9 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G B 9 " -0.011 2.00e-02 2.50e+03 pdb=" C5 G B 9 " 0.009 2.00e-02 2.50e+03 pdb=" C6 G B 9 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G B 9 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G B 9 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G B 9 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G B 9 " -0.012 2.00e-02 2.50e+03 pdb=" N3 G B 9 " 0.011 2.00e-02 2.50e+03 pdb=" C4 G B 9 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 566 " 0.026 2.00e-02 2.50e+03 1.45e-02 4.18e+00 pdb=" CG TYR A 566 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR A 566 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 566 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 566 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 566 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 566 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR A 566 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 7 " -0.024 2.00e-02 2.50e+03 1.03e-02 2.92e+00 pdb=" N9 A B 7 " 0.018 2.00e-02 2.50e+03 pdb=" C8 A B 7 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A B 7 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A B 7 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A B 7 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 7 " -0.010 2.00e-02 2.50e+03 pdb=" N1 A B 7 " -0.008 2.00e-02 2.50e+03 pdb=" C2 A B 7 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A B 7 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A B 7 " 0.006 2.00e-02 2.50e+03 ... (remaining 991 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1243 2.81 - 3.33: 5567 3.33 - 3.86: 9870 3.86 - 4.38: 11248 4.38 - 4.90: 19078 Nonbonded interactions: 47006 Sorted by model distance: nonbonded pdb=" O LYS A 723 " pdb=" OG1 THR A 727 " model vdw 2.288 3.040 nonbonded pdb=" O GLU A 503 " pdb=" OG1 THR A 506 " model vdw 2.346 3.040 nonbonded pdb=" O HIS A 557 " pdb=" OH TYR A 715 " model vdw 2.364 3.040 nonbonded pdb=" O PHE A 789 " pdb=" OG SER A 793 " model vdw 2.365 3.040 nonbonded pdb=" OD1 ASP A 392 " pdb=" NH2 ARG A 791 " model vdw 2.414 3.120 ... (remaining 47001 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.480 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:3.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.011 0.045 6158 Z= 0.704 Angle : 1.168 8.457 8421 Z= 0.849 Chirality : 0.069 0.290 956 Planarity : 0.004 0.024 994 Dihedral : 16.440 88.252 2499 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.82 % Allowed : 12.66 % Favored : 86.51 % 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: -3.00 (0.27), residues: 680 helix: -0.59 (0.25), residues: 300 sheet: -3.23 (0.48), residues: 90 loop : -3.09 (0.27), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP A 873 HIS 0.010 0.003 HIS A 876 PHE 0.016 0.004 PHE A 388 TYR 0.026 0.004 TYR A 566 ARG 0.008 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 138 time to evaluate : 0.799 Fit side-chains REVERT: A 272 PHE cc_start: 0.8675 (t80) cc_final: 0.8435 (t80) REVERT: A 279 GLU cc_start: 0.8652 (tp30) cc_final: 0.8441 (tp30) REVERT: A 283 LYS cc_start: 0.8818 (mtpm) cc_final: 0.8608 (mtpp) REVERT: A 435 ASP cc_start: 0.8367 (t70) cc_final: 0.7873 (t70) REVERT: A 613 ASP cc_start: 0.7795 (t70) cc_final: 0.7566 (t0) REVERT: A 679 LYS cc_start: 0.7585 (tppt) cc_final: 0.7367 (tttt) REVERT: A 732 ARG cc_start: 0.6464 (ptt90) cc_final: 0.5340 (ptm160) REVERT: A 758 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8201 (tm-30) REVERT: A 889 ILE cc_start: 0.8863 (tp) cc_final: 0.8458 (tp) REVERT: A 895 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7778 (tm-30) outliers start: 5 outliers final: 2 residues processed: 142 average time/residue: 0.2273 time to fit residues: 40.6204 Evaluate side-chains 81 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 324 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 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 289 GLN A 299 GLN A 305 GLN A 336 GLN A 354 ASN A 381 HIS A 384 ASN A 501 ASN A 517 GLN A 608 ASN A 619 GLN A 623 HIS A 769 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104418 restraints weight = 8191.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.107726 restraints weight = 4803.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.109927 restraints weight = 3382.937| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6158 Z= 0.207 Angle : 0.526 7.947 8421 Z= 0.261 Chirality : 0.038 0.144 956 Planarity : 0.003 0.031 994 Dihedral : 14.415 73.562 1108 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.12 % Allowed : 13.82 % Favored : 83.06 % 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 (0.31), residues: 680 helix: 1.05 (0.29), residues: 307 sheet: -3.01 (0.48), residues: 99 loop : -2.70 (0.31), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 646 HIS 0.007 0.001 HIS A 623 PHE 0.026 0.002 PHE A 685 TYR 0.011 0.001 TYR A 383 ARG 0.004 0.001 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.635 Fit side-chains REVERT: A 283 LYS cc_start: 0.8734 (mtpm) cc_final: 0.8267 (mttp) REVERT: A 435 ASP cc_start: 0.8447 (t70) cc_final: 0.7873 (t70) REVERT: A 454 TYR cc_start: 0.7053 (OUTLIER) cc_final: 0.6700 (m-10) REVERT: A 613 ASP cc_start: 0.7722 (t70) cc_final: 0.7512 (t70) REVERT: A 732 ARG cc_start: 0.6605 (ptt90) cc_final: 0.5808 (ptm160) REVERT: A 754 ASN cc_start: 0.7845 (m-40) cc_final: 0.7609 (m-40) REVERT: A 758 GLU cc_start: 0.8476 (tm-30) cc_final: 0.7992 (tm-30) REVERT: A 805 ASN cc_start: 0.7497 (t0) cc_final: 0.7198 (t0) REVERT: A 889 ILE cc_start: 0.9232 (tp) cc_final: 0.8944 (tp) REVERT: A 895 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7327 (tm-30) REVERT: A 907 LYS cc_start: 0.8945 (mttt) cc_final: 0.8729 (mttm) outliers start: 19 outliers final: 13 residues processed: 94 average time/residue: 0.1737 time to fit residues: 22.0413 Evaluate side-chains 81 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 HIS A 623 HIS A 678 GLN A 708 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.120671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.098501 restraints weight = 8464.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.101661 restraints weight = 4944.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.103820 restraints weight = 3542.882| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6158 Z= 0.284 Angle : 0.554 6.897 8421 Z= 0.276 Chirality : 0.040 0.141 956 Planarity : 0.003 0.034 994 Dihedral : 14.201 73.375 1105 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 3.95 % Allowed : 13.32 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.32), residues: 680 helix: 1.48 (0.30), residues: 307 sheet: -3.16 (0.48), residues: 93 loop : -2.58 (0.32), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 771 HIS 0.006 0.001 HIS A 623 PHE 0.023 0.002 PHE A 685 TYR 0.013 0.002 TYR A 622 ARG 0.008 0.001 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.648 Fit side-chains REVERT: A 425 ASP cc_start: 0.7667 (t0) cc_final: 0.7462 (t0) REVERT: A 454 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6774 (m-80) REVERT: A 584 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7184 (mt0) REVERT: A 613 ASP cc_start: 0.7845 (t70) cc_final: 0.7507 (t70) REVERT: A 620 GLU cc_start: 0.8108 (tp30) cc_final: 0.7613 (tp30) REVERT: A 758 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8053 (tm-30) REVERT: A 760 MET cc_start: 0.8568 (ttp) cc_final: 0.8093 (ttm) REVERT: A 889 ILE cc_start: 0.9260 (tp) cc_final: 0.8996 (tp) REVERT: A 895 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7471 (tm-30) outliers start: 24 outliers final: 14 residues processed: 86 average time/residue: 0.1604 time to fit residues: 19.1557 Evaluate side-chains 72 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 6 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.122124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.100113 restraints weight = 8488.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.103321 restraints weight = 4902.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.105494 restraints weight = 3493.475| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6158 Z= 0.200 Angle : 0.506 6.393 8421 Z= 0.253 Chirality : 0.039 0.214 956 Planarity : 0.003 0.033 994 Dihedral : 14.265 73.606 1105 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.45 % Allowed : 15.13 % Favored : 81.41 % 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: -0.78 (0.33), residues: 680 helix: 1.85 (0.30), residues: 306 sheet: -3.12 (0.49), residues: 88 loop : -2.38 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 512 HIS 0.007 0.001 HIS A 623 PHE 0.018 0.001 PHE A 685 TYR 0.010 0.001 TYR A 383 ARG 0.006 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.586 Fit side-chains REVERT: A 425 ASP cc_start: 0.7644 (t0) cc_final: 0.7440 (t0) REVERT: A 454 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.6776 (m-80) REVERT: A 613 ASP cc_start: 0.7817 (t70) cc_final: 0.7503 (t70) REVERT: A 754 ASN cc_start: 0.7800 (m-40) cc_final: 0.7534 (m-40) REVERT: A 758 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8006 (tm-30) REVERT: A 889 ILE cc_start: 0.9272 (tp) cc_final: 0.8994 (tp) REVERT: A 895 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7495 (tm-30) outliers start: 21 outliers final: 15 residues processed: 78 average time/residue: 0.1455 time to fit residues: 16.1019 Evaluate side-chains 70 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 0.0770 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.120761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098888 restraints weight = 8428.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.102052 restraints weight = 4849.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.104068 restraints weight = 3457.905| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6158 Z= 0.214 Angle : 0.507 6.426 8421 Z= 0.254 Chirality : 0.040 0.229 956 Planarity : 0.003 0.033 994 Dihedral : 14.198 73.578 1105 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 3.62 % Allowed : 16.12 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.69 (0.33), residues: 680 helix: 2.01 (0.30), residues: 305 sheet: -3.30 (0.45), residues: 93 loop : -2.32 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 512 HIS 0.008 0.001 HIS A 623 PHE 0.015 0.001 PHE A 853 TYR 0.010 0.001 TYR A 383 ARG 0.008 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.686 Fit side-chains REVERT: A 425 ASP cc_start: 0.7659 (t0) cc_final: 0.7448 (t0) REVERT: A 454 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6816 (m-80) REVERT: A 754 ASN cc_start: 0.7820 (m-40) cc_final: 0.7542 (m-40) REVERT: A 758 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8085 (tm-30) REVERT: A 889 ILE cc_start: 0.9276 (tp) cc_final: 0.9015 (tp) REVERT: A 895 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7433 (tm-30) outliers start: 22 outliers final: 15 residues processed: 78 average time/residue: 0.1470 time to fit residues: 16.4356 Evaluate side-chains 74 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.100060 restraints weight = 8350.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.103271 restraints weight = 4857.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.105428 restraints weight = 3473.666| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6158 Z= 0.182 Angle : 0.500 6.220 8421 Z= 0.249 Chirality : 0.039 0.244 956 Planarity : 0.003 0.033 994 Dihedral : 14.195 73.602 1105 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.62 % Allowed : 16.94 % Favored : 79.44 % 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: -0.52 (0.33), residues: 680 helix: 2.14 (0.30), residues: 305 sheet: -2.90 (0.48), residues: 93 loop : -2.36 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 512 HIS 0.008 0.001 HIS A 623 PHE 0.012 0.001 PHE A 853 TYR 0.017 0.001 TYR A 622 ARG 0.007 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.719 Fit side-chains REVERT: A 425 ASP cc_start: 0.7659 (t0) cc_final: 0.7450 (t0) REVERT: A 454 TYR cc_start: 0.7289 (OUTLIER) cc_final: 0.6834 (m-80) REVERT: A 754 ASN cc_start: 0.7754 (m-40) cc_final: 0.7554 (m-40) REVERT: A 758 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8075 (tm-30) REVERT: A 889 ILE cc_start: 0.9295 (tp) cc_final: 0.9026 (tp) outliers start: 22 outliers final: 17 residues processed: 80 average time/residue: 0.1673 time to fit residues: 19.5022 Evaluate side-chains 74 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 0.0670 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.121942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.099791 restraints weight = 8408.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102952 restraints weight = 4883.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.105006 restraints weight = 3491.971| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6158 Z= 0.185 Angle : 0.507 7.277 8421 Z= 0.251 Chirality : 0.040 0.257 956 Planarity : 0.003 0.033 994 Dihedral : 14.144 73.591 1105 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.78 % Allowed : 17.11 % Favored : 79.11 % 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: -0.40 (0.34), residues: 680 helix: 2.16 (0.30), residues: 306 sheet: -2.73 (0.50), residues: 93 loop : -2.24 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 512 HIS 0.009 0.001 HIS A 623 PHE 0.012 0.001 PHE A 459 TYR 0.023 0.001 TYR A 622 ARG 0.007 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.607 Fit side-chains REVERT: A 425 ASP cc_start: 0.7660 (t0) cc_final: 0.7451 (t0) REVERT: A 454 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.6765 (m-80) REVERT: A 758 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8037 (tm-30) REVERT: A 889 ILE cc_start: 0.9289 (tp) cc_final: 0.9025 (tp) REVERT: A 895 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7479 (tm-30) outliers start: 23 outliers final: 16 residues processed: 75 average time/residue: 0.1389 time to fit residues: 15.3553 Evaluate side-chains 73 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 853 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 49 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.119010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.097566 restraints weight = 8383.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100541 restraints weight = 4804.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.102686 restraints weight = 3444.137| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6158 Z= 0.226 Angle : 0.529 6.206 8421 Z= 0.263 Chirality : 0.040 0.270 956 Planarity : 0.003 0.035 994 Dihedral : 14.096 73.586 1105 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.95 % Allowed : 16.78 % Favored : 79.28 % 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: -0.47 (0.33), residues: 680 helix: 2.11 (0.30), residues: 306 sheet: -2.69 (0.45), residues: 108 loop : -2.24 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 512 HIS 0.009 0.001 HIS A 623 PHE 0.015 0.001 PHE A 853 TYR 0.023 0.001 TYR A 622 ARG 0.006 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 0.784 Fit side-chains REVERT: A 454 TYR cc_start: 0.7344 (OUTLIER) cc_final: 0.6794 (m-80) REVERT: A 754 ASN cc_start: 0.7757 (m-40) cc_final: 0.7494 (m-40) REVERT: A 758 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8049 (tm-30) REVERT: A 822 ASP cc_start: 0.9074 (OUTLIER) cc_final: 0.8160 (p0) REVERT: A 889 ILE cc_start: 0.9291 (tp) cc_final: 0.9039 (tp) outliers start: 24 outliers final: 17 residues processed: 72 average time/residue: 0.1414 time to fit residues: 14.7752 Evaluate side-chains 74 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 853 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 60 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.120365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.099023 restraints weight = 8421.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.102169 restraints weight = 4770.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.104392 restraints weight = 3377.412| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6158 Z= 0.185 Angle : 0.521 7.382 8421 Z= 0.257 Chirality : 0.040 0.284 956 Planarity : 0.003 0.034 994 Dihedral : 14.105 73.611 1105 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.45 % Allowed : 17.76 % Favored : 78.78 % 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: -0.35 (0.34), residues: 680 helix: 2.18 (0.30), residues: 306 sheet: -2.60 (0.45), residues: 108 loop : -2.16 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 512 HIS 0.010 0.001 HIS A 623 PHE 0.012 0.001 PHE A 853 TYR 0.023 0.001 TYR A 622 ARG 0.006 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.691 Fit side-chains REVERT: A 454 TYR cc_start: 0.7355 (OUTLIER) cc_final: 0.6801 (m-80) REVERT: A 754 ASN cc_start: 0.7745 (m-40) cc_final: 0.7484 (m-40) REVERT: A 758 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8042 (tm-30) REVERT: A 822 ASP cc_start: 0.9037 (OUTLIER) cc_final: 0.8156 (p0) REVERT: A 889 ILE cc_start: 0.9294 (tp) cc_final: 0.9035 (tp) REVERT: A 895 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7545 (tm-30) outliers start: 21 outliers final: 17 residues processed: 75 average time/residue: 0.1357 time to fit residues: 15.0492 Evaluate side-chains 77 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 853 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 61 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 0.0070 chunk 69 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.118812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.096630 restraints weight = 8563.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.099714 restraints weight = 4993.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.101742 restraints weight = 3591.691| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6158 Z= 0.258 Angle : 0.560 7.705 8421 Z= 0.279 Chirality : 0.041 0.293 956 Planarity : 0.004 0.036 994 Dihedral : 14.069 73.528 1105 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 3.95 % Allowed : 17.11 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.33), residues: 680 helix: 2.01 (0.30), residues: 307 sheet: -2.65 (0.45), residues: 108 loop : -2.24 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 512 HIS 0.010 0.001 HIS A 623 PHE 0.017 0.001 PHE A 853 TYR 0.023 0.002 TYR A 622 ARG 0.007 0.001 ARG A 811 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 0.529 Fit side-chains REVERT: A 454 TYR cc_start: 0.7386 (OUTLIER) cc_final: 0.6791 (m-80) REVERT: A 754 ASN cc_start: 0.7773 (m-40) cc_final: 0.7506 (m-40) REVERT: A 758 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8050 (tm-30) REVERT: A 822 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8148 (p0) REVERT: A 889 ILE cc_start: 0.9297 (tp) cc_final: 0.9048 (tp) outliers start: 24 outliers final: 17 residues processed: 72 average time/residue: 0.1560 time to fit residues: 16.0189 Evaluate side-chains 73 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 853 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.119942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097720 restraints weight = 8623.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.100885 restraints weight = 5000.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.102971 restraints weight = 3576.003| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6158 Z= 0.203 Angle : 0.537 7.229 8421 Z= 0.266 Chirality : 0.040 0.302 956 Planarity : 0.003 0.034 994 Dihedral : 14.108 73.608 1105 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 3.45 % Allowed : 17.43 % Favored : 79.11 % 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: -0.41 (0.34), residues: 680 helix: 2.09 (0.30), residues: 307 sheet: -2.58 (0.46), residues: 108 loop : -2.18 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 512 HIS 0.010 0.001 HIS A 623 PHE 0.014 0.001 PHE A 579 TYR 0.022 0.001 TYR A 622 ARG 0.006 0.000 ARG A 811 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1882.73 seconds wall clock time: 34 minutes 46.15 seconds (2086.15 seconds total)