Starting phenix.real_space_refine on Thu Jul 2 03:21:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7to0_26025/07_2026/7to0_26025.cif Found real_map, /net/cci-nas-00/data/ceres_data/7to0_26025/07_2026/7to0_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7to0_26025/07_2026/7to0_26025.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7to0_26025/07_2026/7to0_26025.cif" model { file = "/net/cci-nas-00/data/ceres_data/7to0_26025/07_2026/7to0_26025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7to0_26025/07_2026/7to0_26025.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7to0_26025/07_2026/7to0_26025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7to0_26025/07_2026/7to0_26025.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 1.56, per 1000 atoms: 0.26 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: 0.54 Conformation dependent library (CDL) restraints added in 433.5 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: 0.67 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: 1.20 Time building geometry restraints manager: 0.75 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: 3319 17.65 - 35.30: 296 35.30 - 52.95: 75 52.95 - 70.60: 9 70.60 - 88.25: 6 Dihedral angle restraints: 3705 sinusoidal: 1703 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 3702 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: 0.930 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.140 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 0.014 0.418 6161 Z= 0.865 Angle : 1.168 8.457 8421 Z= 0.849 Chirality : 0.069 0.290 956 Planarity : 0.004 0.024 994 Dihedral : 14.218 88.252 2405 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.001 ARG A 466 TYR 0.026 0.004 TYR A 566 PHE 0.016 0.004 PHE A 388 TRP 0.016 0.004 TRP A 873 HIS 0.010 0.003 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.01096 / 0.81 ( 6158) covalent geometry : angle 1.16819 / 0.85 ( 8421) hydrogen bonds : bond 0.12240 / 7.78 ( 266) hydrogen bonds : angle 5.04160 / 3.50 ( 754) metal coordination : bond 0.40450 / 20.30 ( 3) *********************** 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 : 0.247 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: 0.7796 (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: 0.0975 time to fit residues: 17.6054 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 : 0.224 ------------------------------------------------------------------------------- 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 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 678 GLN A 769 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.125792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.104073 restraints weight = 8288.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.107309 restraints weight = 4845.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.109513 restraints weight = 3435.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.110810 restraints weight = 2724.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.111951 restraints weight = 2352.221| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6161 Z= 0.136 Angle : 0.530 8.296 8421 Z= 0.264 Chirality : 0.039 0.146 956 Planarity : 0.003 0.031 994 Dihedral : 6.680 71.681 1014 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.29 % Allowed : 13.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.31), residues: 680 helix: 1.04 (0.29), residues: 307 sheet: -3.01 (0.48), residues: 99 loop : -2.69 (0.31), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 811 TYR 0.012 0.001 TYR A 383 PHE 0.026 0.001 PHE A 685 TRP 0.007 0.001 TRP A 646 HIS 0.007 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 6158) covalent geometry : angle 0.53036 / 0.26 ( 8421) hydrogen bonds : bond 0.03375 / 2.22 ( 266) hydrogen bonds : angle 3.57050 / 2.45 ( 754) metal coordination : bond 0.00819 / 0.42 ( 3) *********************** 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: 20 poor density : 84 time to evaluate : 0.238 Fit side-chains REVERT: A 283 LYS cc_start: 0.8713 (mtpm) cc_final: 0.8258 (mttp) REVERT: A 435 ASP cc_start: 0.8442 (t70) cc_final: 0.7808 (t70) REVERT: A 454 TYR cc_start: 0.6962 (OUTLIER) cc_final: 0.6634 (m-10) REVERT: A 613 ASP cc_start: 0.7676 (t70) cc_final: 0.7472 (t70) REVERT: A 732 ARG cc_start: 0.6597 (ptt90) cc_final: 0.5853 (ptm160) REVERT: A 758 GLU cc_start: 0.8471 (tm-30) cc_final: 0.7988 (tm-30) REVERT: A 805 ASN cc_start: 0.7498 (t0) cc_final: 0.7195 (t0) REVERT: A 889 ILE cc_start: 0.9235 (tp) cc_final: 0.8952 (tp) REVERT: A 895 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7560 (tm-30) REVERT: A 907 LYS cc_start: 0.8947 (mttt) cc_final: 0.8730 (mttm) outliers start: 20 outliers final: 14 residues processed: 94 average time/residue: 0.0720 time to fit residues: 9.3383 Evaluate side-chains 82 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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 442 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 32 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 61 optimal weight: 0.4980 chunk 46 optimal weight: 0.0270 chunk 60 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 708 GLN A 794 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.125883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.103712 restraints weight = 8303.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.106947 restraints weight = 4832.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.109044 restraints weight = 3450.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.110657 restraints weight = 2769.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111615 restraints weight = 2355.533| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6161 Z= 0.108 Angle : 0.485 6.788 8421 Z= 0.239 Chirality : 0.037 0.154 956 Planarity : 0.003 0.031 994 Dihedral : 6.354 70.580 1011 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.62 % Allowed : 13.49 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.32), residues: 680 helix: 1.66 (0.30), residues: 307 sheet: -2.93 (0.50), residues: 88 loop : -2.48 (0.32), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 811 TYR 0.011 0.001 TYR A 622 PHE 0.019 0.001 PHE A 685 TRP 0.006 0.001 TRP A 512 HIS 0.007 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 6158) covalent geometry : angle 0.48491 / 0.24 ( 8421) hydrogen bonds : bond 0.03172 / 2.07 ( 266) hydrogen bonds : angle 3.46137 / 2.37 ( 754) metal coordination : bond 0.00179 / 0.09 ( 3) *********************** 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: 22 poor density : 72 time to evaluate : 0.226 Fit side-chains REVERT: A 277 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8900 (mp) REVERT: A 435 ASP cc_start: 0.8415 (t70) cc_final: 0.7777 (t70) REVERT: A 454 TYR cc_start: 0.6948 (OUTLIER) cc_final: 0.6608 (m-10) REVERT: A 584 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.6989 (mt0) REVERT: A 613 ASP cc_start: 0.7720 (t70) cc_final: 0.7443 (t70) REVERT: A 758 GLU cc_start: 0.8551 (tm-30) cc_final: 0.7990 (tm-30) REVERT: A 889 ILE cc_start: 0.9242 (tp) cc_final: 0.8948 (tp) REVERT: A 895 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7495 (tm-30) outliers start: 22 outliers final: 13 residues processed: 87 average time/residue: 0.0603 time to fit residues: 7.4026 Evaluate side-chains 77 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 408 LEU 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 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 766 LEU 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 18 optimal weight: 0.9980 chunk 46 optimal weight: 0.0070 chunk 45 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 44 optimal weight: 0.2980 chunk 43 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.126108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.103625 restraints weight = 8261.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106905 restraints weight = 4795.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.109201 restraints weight = 3408.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.110607 restraints weight = 2709.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.111779 restraints weight = 2331.774| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6161 Z= 0.092 Angle : 0.469 7.006 8421 Z= 0.232 Chirality : 0.038 0.219 956 Planarity : 0.003 0.030 994 Dihedral : 6.185 69.155 1011 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.29 % Allowed : 14.31 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.33), residues: 680 helix: 2.04 (0.30), residues: 306 sheet: -2.79 (0.49), residues: 95 loop : -2.35 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 575 TYR 0.008 0.001 TYR A 383 PHE 0.016 0.001 PHE A 685 TRP 0.005 0.001 TRP A 512 HIS 0.008 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 ( 6158) covalent geometry : angle 0.46870 / 0.23 ( 8421) hydrogen bonds : bond 0.03012 / 1.97 ( 266) hydrogen bonds : angle 3.37658 / 2.33 ( 754) metal coordination : bond 0.00091 / 0.04 ( 3) *********************** 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 88 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.220 Fit side-chains REVERT: A 454 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.6607 (m-10) REVERT: A 613 ASP cc_start: 0.7756 (t70) cc_final: 0.7468 (t70) REVERT: A 754 ASN cc_start: 0.7694 (m-40) cc_final: 0.7477 (m-40) REVERT: A 758 GLU cc_start: 0.8570 (tm-30) cc_final: 0.7939 (tm-30) REVERT: A 889 ILE cc_start: 0.9232 (tp) cc_final: 0.8957 (tp) REVERT: A 895 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7402 (tm-30) outliers start: 20 outliers final: 14 residues processed: 79 average time/residue: 0.0564 time to fit residues: 6.6723 Evaluate side-chains 72 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 321 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 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 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 15 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 557 HIS A 726 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.101701 restraints weight = 8433.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.105027 restraints weight = 4853.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.107252 restraints weight = 3431.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.108746 restraints weight = 2727.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.109592 restraints weight = 2325.133| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6161 Z= 0.124 Angle : 0.507 8.495 8421 Z= 0.247 Chirality : 0.039 0.231 956 Planarity : 0.003 0.032 994 Dihedral : 5.969 66.272 1011 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.45 % Allowed : 14.47 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.33), residues: 680 helix: 2.17 (0.30), residues: 305 sheet: -2.94 (0.51), residues: 88 loop : -2.24 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 811 TYR 0.009 0.001 TYR A 383 PHE 0.016 0.001 PHE A 685 TRP 0.005 0.001 TRP A 512 HIS 0.006 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 ( 6158) covalent geometry : angle 0.50717 / 0.25 ( 8421) hydrogen bonds : bond 0.03273 / 2.14 ( 266) hydrogen bonds : angle 3.46768 / 2.38 ( 754) metal coordination : bond 0.00182 / 0.09 ( 3) *********************** 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 85 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.173 Fit side-chains REVERT: A 454 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.6731 (m-10) REVERT: A 758 GLU cc_start: 0.8605 (tm-30) cc_final: 0.7997 (tm-30) REVERT: A 889 ILE cc_start: 0.9284 (tp) cc_final: 0.9003 (tp) REVERT: A 895 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7457 (tm-30) outliers start: 21 outliers final: 14 residues processed: 76 average time/residue: 0.0530 time to fit residues: 5.7593 Evaluate side-chains 74 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 321 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 629 ILE 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 766 LEU 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 37 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 1 optimal weight: 0.1980 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.121867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.099628 restraints weight = 8445.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102847 restraints weight = 4910.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.105040 restraints weight = 3512.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.106406 restraints weight = 2814.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.107413 restraints weight = 2431.259| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6161 Z= 0.150 Angle : 0.532 7.398 8421 Z= 0.261 Chirality : 0.040 0.242 956 Planarity : 0.003 0.033 994 Dihedral : 5.924 63.623 1011 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 4.28 % Allowed : 15.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.33), residues: 680 helix: 2.16 (0.30), residues: 306 sheet: -2.88 (0.49), residues: 93 loop : -2.26 (0.33), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 811 TYR 0.010 0.001 TYR A 383 PHE 0.015 0.001 PHE A 853 TRP 0.005 0.001 TRP A 512 HIS 0.008 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 6158) covalent geometry : angle 0.53248 / 0.26 ( 8421) hydrogen bonds : bond 0.03411 / 2.22 ( 266) hydrogen bonds : angle 3.60065 / 2.46 ( 754) metal coordination : bond 0.00239 / 0.12 ( 3) *********************** 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 85 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.225 Fit side-chains REVERT: A 454 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6845 (m-80) REVERT: A 479 MET cc_start: 0.8276 (mtm) cc_final: 0.7942 (mtm) REVERT: A 754 ASN cc_start: 0.7832 (m-40) cc_final: 0.7562 (m-40) REVERT: A 758 GLU cc_start: 0.8638 (tm-30) cc_final: 0.7996 (tm-30) REVERT: A 889 ILE cc_start: 0.9273 (tp) cc_final: 0.9001 (tp) outliers start: 26 outliers final: 17 residues processed: 75 average time/residue: 0.0524 time to fit residues: 5.9083 Evaluate side-chains 69 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 321 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 629 ILE Chi-restraints excluded: chain A residue 643 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.122619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.100429 restraints weight = 8414.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.103701 restraints weight = 4878.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.105829 restraints weight = 3472.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.107372 restraints weight = 2789.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.108332 restraints weight = 2390.090| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6161 Z= 0.131 Angle : 0.521 7.510 8421 Z= 0.256 Chirality : 0.040 0.258 956 Planarity : 0.003 0.034 994 Dihedral : 5.850 62.153 1011 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.34), residues: 680 helix: 2.22 (0.30), residues: 306 sheet: -2.54 (0.50), residues: 98 loop : -2.25 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 488 TYR 0.010 0.001 TYR A 715 PHE 0.013 0.001 PHE A 459 TRP 0.005 0.001 TRP A 512 HIS 0.008 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 6158) covalent geometry : angle 0.52064 / 0.26 ( 8421) hydrogen bonds : bond 0.03311 / 2.17 ( 266) hydrogen bonds : angle 3.53021 / 2.42 ( 754) metal coordination : bond 0.00177 / 0.09 ( 3) *********************** 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: 24 poor density : 59 time to evaluate : 0.223 Fit side-chains REVERT: A 454 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.6826 (m-80) REVERT: A 754 ASN cc_start: 0.7815 (m-40) cc_final: 0.7557 (m-40) REVERT: A 758 GLU cc_start: 0.8625 (tm-30) cc_final: 0.7992 (tm-30) REVERT: A 889 ILE cc_start: 0.9269 (tp) cc_final: 0.8997 (tp) REVERT: A 895 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7540 (tm-30) outliers start: 24 outliers final: 17 residues processed: 74 average time/residue: 0.0542 time to fit residues: 5.8052 Evaluate side-chains 72 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 321 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 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 781 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 12 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 0.0980 chunk 46 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 41 optimal weight: 0.0570 chunk 50 optimal weight: 3.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 ASN A 623 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.124204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.102176 restraints weight = 8378.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.105504 restraints weight = 4820.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107714 restraints weight = 3411.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.109186 restraints weight = 2726.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.110296 restraints weight = 2333.773| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6161 Z= 0.102 Angle : 0.507 7.530 8421 Z= 0.248 Chirality : 0.039 0.274 956 Planarity : 0.003 0.033 994 Dihedral : 5.724 60.241 1011 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.29 % Allowed : 17.11 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.34), residues: 680 helix: 2.32 (0.30), residues: 306 sheet: -2.37 (0.51), residues: 98 loop : -2.14 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 488 TYR 0.010 0.001 TYR A 715 PHE 0.011 0.001 PHE A 459 TRP 0.005 0.001 TRP A 512 HIS 0.009 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 6158) covalent geometry : angle 0.50748 / 0.25 ( 8421) hydrogen bonds : bond 0.03081 / 2.01 ( 266) hydrogen bonds : angle 3.46609 / 2.39 ( 754) metal coordination : bond 0.00129 / 0.06 ( 3) *********************** 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 80 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.220 Fit side-chains REVERT: A 454 TYR cc_start: 0.7229 (OUTLIER) cc_final: 0.6819 (m-80) REVERT: A 754 ASN cc_start: 0.7710 (m-40) cc_final: 0.7450 (m-40) REVERT: A 758 GLU cc_start: 0.8611 (tm-30) cc_final: 0.7978 (tm-30) REVERT: A 889 ILE cc_start: 0.9271 (tp) cc_final: 0.8986 (tp) REVERT: A 895 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7579 (tm-30) outliers start: 20 outliers final: 16 residues processed: 71 average time/residue: 0.0479 time to fit residues: 5.0730 Evaluate side-chains 71 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 345 ILE 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 643 LEU Chi-restraints excluded: chain A residue 653 LEU 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 853 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 17 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 0.0040 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.123368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.101008 restraints weight = 8466.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.104330 restraints weight = 4918.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.106411 restraints weight = 3503.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.108044 restraints weight = 2814.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.109084 restraints weight = 2402.147| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6161 Z= 0.116 Angle : 0.522 7.476 8421 Z= 0.256 Chirality : 0.039 0.282 956 Planarity : 0.003 0.034 994 Dihedral : 5.639 57.501 1011 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.45 % Allowed : 17.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.34), residues: 680 helix: 2.33 (0.30), residues: 305 sheet: -2.30 (0.52), residues: 98 loop : -2.14 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 488 TYR 0.010 0.001 TYR A 390 PHE 0.010 0.001 PHE A 459 TRP 0.005 0.001 TRP A 512 HIS 0.010 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 6158) covalent geometry : angle 0.52198 / 0.26 ( 8421) hydrogen bonds : bond 0.03176 / 2.07 ( 266) hydrogen bonds : angle 3.53856 / 2.44 ( 754) metal coordination : bond 0.00151 / 0.07 ( 3) *********************** 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 80 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.216 Fit side-chains REVERT: A 454 TYR cc_start: 0.7265 (OUTLIER) cc_final: 0.6769 (m-80) REVERT: A 754 ASN cc_start: 0.7816 (m-40) cc_final: 0.7548 (m-40) REVERT: A 758 GLU cc_start: 0.8617 (tm-30) cc_final: 0.7984 (tm-30) REVERT: A 889 ILE cc_start: 0.9284 (tp) cc_final: 0.9005 (tp) REVERT: A 895 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7584 (tm-30) outliers start: 21 outliers final: 17 residues processed: 71 average time/residue: 0.0559 time to fit residues: 5.9659 Evaluate side-chains 73 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 321 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 66 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.120749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.098577 restraints weight = 8484.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.101816 restraints weight = 4933.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.103969 restraints weight = 3514.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.105349 restraints weight = 2814.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.106403 restraints weight = 2428.112| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6161 Z= 0.140 Angle : 0.543 7.508 8421 Z= 0.266 Chirality : 0.040 0.292 956 Planarity : 0.003 0.034 994 Dihedral : 5.658 54.053 1011 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.45 % Allowed : 16.94 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.34), residues: 680 helix: 2.24 (0.30), residues: 305 sheet: -2.34 (0.51), residues: 98 loop : -2.14 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 488 TYR 0.010 0.001 TYR A 715 PHE 0.012 0.001 PHE A 853 TRP 0.005 0.001 TRP A 512 HIS 0.010 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 6158) covalent geometry : angle 0.54254 / 0.27 ( 8421) hydrogen bonds : bond 0.03344 / 2.19 ( 266) hydrogen bonds : angle 3.61796 / 2.49 ( 754) metal coordination : bond 0.00194 / 0.09 ( 3) ********************** 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 80 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.230 Fit side-chains REVERT: A 454 TYR cc_start: 0.7274 (OUTLIER) cc_final: 0.6852 (m-80) REVERT: A 754 ASN cc_start: 0.7842 (m-40) cc_final: 0.7563 (m-40) REVERT: A 758 GLU cc_start: 0.8563 (tm-30) cc_final: 0.7995 (tm-30) REVERT: A 889 ILE cc_start: 0.9297 (tp) cc_final: 0.9029 (tp) outliers start: 21 outliers final: 16 residues processed: 71 average time/residue: 0.0553 time to fit residues: 5.8824 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 : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 321 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 55 optimal weight: 0.0980 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 0.0060 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.102323 restraints weight = 8331.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.105698 restraints weight = 4798.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.107891 restraints weight = 3378.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.109258 restraints weight = 2693.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.110427 restraints weight = 2323.914| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6161 Z= 0.100 Angle : 0.519 8.023 8421 Z= 0.252 Chirality : 0.039 0.298 956 Planarity : 0.003 0.033 994 Dihedral : 5.559 52.101 1011 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.34), residues: 680 helix: 2.34 (0.30), residues: 305 sheet: -2.32 (0.51), residues: 100 loop : -2.03 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 488 TYR 0.010 0.001 TYR A 715 PHE 0.010 0.001 PHE A 685 TRP 0.005 0.001 TRP A 512 HIS 0.010 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 6158) covalent geometry : angle 0.51944 / 0.25 ( 8421) hydrogen bonds : bond 0.03098 / 2.01 ( 266) hydrogen bonds : angle 3.52514 / 2.43 ( 754) metal coordination : bond 0.00109 / 0.05 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1005.81 seconds wall clock time: 18 minutes 6.86 seconds (1086.86 seconds total)