Starting phenix.real_space_refine on Thu Jul 2 08:25:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rvz_54293/07_2026/9rvz_54293.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rvz_54293/07_2026/9rvz_54293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rvz_54293/07_2026/9rvz_54293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rvz_54293/07_2026/9rvz_54293.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rvz_54293/07_2026/9rvz_54293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rvz_54293/07_2026/9rvz_54293.map" } resolution = 3.2 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 88 5.49 5 S 38 5.16 5 C 4514 2.51 5 N 1323 2.21 5 O 1713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s 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: 7676 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 432 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 434 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3711 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 450} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1249 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain breaks: 1 Chain: "E" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 925 Classifications: {'RNA': 44} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 21, 'rna3p_pyr': 21} Link IDs: {'rna2p': 2, 'rna3p': 41} Chain: "F" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 925 Classifications: {'RNA': 44} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 21, 'rna3p_pyr': 22} Link IDs: {'rna2p': 1, 'rna3p': 42} Time building chain proxies: 1.74, per 1000 atoms: 0.23 Number of scatterers: 7676 At special positions: 0 Unit cell: (81.543, 94.251, 154.614, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 88 15.00 O 1713 8.00 N 1323 7.00 C 4514 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: 0.72 Conformation dependent library (CDL) restraints added in 332.3 milliseconds 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 5 sheets defined 69.8% alpha, 6.4% beta 35 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 695 through 747 removed outlier: 3.603A pdb=" N VAL A 699 " --> pdb=" O CYS A 695 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 747 Processing helix chain 'D' and resid 3 through 25 removed outlier: 3.724A pdb=" N LYS D 24 " --> pdb=" O ARG D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 36 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 43 through 51 Processing helix chain 'D' and resid 53 through 62 Processing helix chain 'D' and resid 95 through 111 removed outlier: 3.657A pdb=" N TYR D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 125 removed outlier: 3.794A pdb=" N HIS D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 129 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 140 through 151 Processing helix chain 'D' and resid 521 through 530 Processing helix chain 'D' and resid 535 through 554 Processing helix chain 'D' and resid 594 through 600 removed outlier: 4.216A pdb=" N THR D 598 " --> pdb=" O PRO D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 608 Processing helix chain 'D' and resid 618 through 629 Processing helix chain 'D' and resid 639 through 652 Processing helix chain 'D' and resid 654 through 658 Processing helix chain 'D' and resid 662 through 670 removed outlier: 3.503A pdb=" N TYR D 670 " --> pdb=" O LEU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 680 removed outlier: 3.773A pdb=" N LYS D 678 " --> pdb=" O ASN D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 688 removed outlier: 4.045A pdb=" N TYR D 685 " --> pdb=" O LEU D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 714 removed outlier: 3.597A pdb=" N MET D 702 " --> pdb=" O THR D 698 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP D 708 " --> pdb=" O TYR D 704 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL D 709 " --> pdb=" O ALA D 705 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS D 714 " --> pdb=" O LEU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 725 Processing helix chain 'D' and resid 729 through 743 Processing helix chain 'D' and resid 746 through 773 removed outlier: 3.932A pdb=" N THR D 773 " --> pdb=" O LYS D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 780 through 787 Processing helix chain 'D' and resid 788 through 790 No H-bonds generated for 'chain 'D' and resid 788 through 790' Processing helix chain 'D' and resid 793 through 801 Processing helix chain 'D' and resid 803 through 816 Processing helix chain 'C' and resid 6 through 25 Processing helix chain 'C' and resid 30 through 36 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 42 through 50 removed outlier: 4.110A pdb=" N MET C 46 " --> pdb=" O PHE C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 63 Processing helix chain 'C' and resid 96 through 110 removed outlier: 3.837A pdb=" N GLN C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 127 removed outlier: 3.815A pdb=" N LEU C 122 " --> pdb=" O PRO C 118 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 138 Processing helix chain 'C' and resid 140 through 151 Processing sheet with id=AA1, first strand: chain 'D' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'D' and resid 117 through 118 Processing sheet with id=AA3, first strand: chain 'D' and resid 531 through 533 removed outlier: 3.641A pdb=" N ILE D 576 " --> pdb=" O PHE D 588 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N PHE D 637 " --> pdb=" O VAL D 611 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS D 613 " --> pdb=" O PHE D 637 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 28 through 29 Processing sheet with id=AA5, first strand: chain 'C' and resid 155 through 158 372 hydrogen bonds defined for protein. 1074 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 1.29 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1121 1.32 - 1.44: 2503 1.44 - 1.56: 4115 1.56 - 1.69: 174 1.69 - 1.81: 63 Bond restraints: 7976 Sorted by residual: bond pdb=" CA ASP D 617 " pdb=" C ASP D 617 " ideal model delta sigma weight residual 1.532 1.477 0.055 9.60e-03 1.09e+04 3.31e+01 bond pdb=" CA HIS C 31 " pdb=" C HIS C 31 " ideal model delta sigma weight residual 1.523 1.456 0.067 1.37e-02 5.33e+03 2.40e+01 bond pdb=" CA ASP D 617 " pdb=" CB ASP D 617 " ideal model delta sigma weight residual 1.533 1.478 0.056 1.37e-02 5.33e+03 1.64e+01 bond pdb=" N ASP D 617 " pdb=" CA ASP D 617 " ideal model delta sigma weight residual 1.462 1.413 0.049 1.31e-02 5.83e+03 1.40e+01 bond pdb=" C TYR D 74 " pdb=" N VAL D 75 " ideal model delta sigma weight residual 1.331 1.384 -0.053 1.43e-02 4.89e+03 1.40e+01 ... (remaining 7971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 11082 3.19 - 6.38: 57 6.38 - 9.57: 1 9.57 - 12.76: 0 12.76 - 15.95: 1 Bond angle restraints: 11141 Sorted by residual: angle pdb=" O3' C E 33 " pdb=" C3' C E 33 " pdb=" C2' C E 33 " ideal model delta sigma weight residual 109.50 125.45 -15.95 1.50e+00 4.44e-01 1.13e+02 angle pdb=" N6 A F 31 " pdb=" C6 A F 31 " pdb=" N1 A F 31 " ideal model delta sigma weight residual 118.60 114.69 3.91 6.00e-01 2.78e+00 4.25e+01 angle pdb=" C3' C E 33 " pdb=" C2' C E 33 " pdb=" O2' C E 33 " ideal model delta sigma weight residual 114.60 123.58 -8.98 1.50e+00 4.44e-01 3.58e+01 angle pdb=" N6 A F 38 " pdb=" C6 A F 38 " pdb=" N1 A F 38 " ideal model delta sigma weight residual 118.60 115.10 3.50 6.00e-01 2.78e+00 3.40e+01 angle pdb=" N6 A F 21 " pdb=" C6 A F 21 " pdb=" N1 A F 21 " ideal model delta sigma weight residual 118.60 115.16 3.44 6.00e-01 2.78e+00 3.29e+01 ... (remaining 11136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.17: 4647 35.17 - 70.35: 248 70.35 - 105.52: 22 105.52 - 140.70: 0 140.70 - 175.87: 2 Dihedral angle restraints: 4919 sinusoidal: 2799 harmonic: 2120 Sorted by residual: dihedral pdb=" C5' C E 33 " pdb=" C4' C E 33 " pdb=" C3' C E 33 " pdb=" O3' C E 33 " ideal model delta sinusoidal sigma weight residual 147.00 55.43 91.57 1 8.00e+00 1.56e-02 1.54e+02 dihedral pdb=" O4' C E 33 " pdb=" C4' C E 33 " pdb=" C3' C E 33 " pdb=" C2' C E 33 " ideal model delta sinusoidal sigma weight residual 24.00 -44.23 68.23 1 8.00e+00 1.56e-02 9.44e+01 dihedral pdb=" C4' C E 33 " pdb=" C3' C E 33 " pdb=" C2' C E 33 " pdb=" C1' C E 33 " ideal model delta sinusoidal sigma weight residual -35.00 32.20 -67.20 1 8.00e+00 1.56e-02 9.19e+01 ... (remaining 4916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 1317 0.161 - 0.321: 4 0.321 - 0.482: 1 0.482 - 0.642: 0 0.642 - 0.803: 1 Chirality restraints: 1323 Sorted by residual: chirality pdb=" C3' C E 33 " pdb=" C4' C E 33 " pdb=" O3' C E 33 " pdb=" C2' C E 33 " both_signs ideal model delta sigma weight residual False -2.74 -1.94 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" CA GLN D 683 " pdb=" N GLN D 683 " pdb=" C GLN D 683 " pdb=" CB GLN D 683 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA ASP D 617 " pdb=" N ASP D 617 " pdb=" C ASP D 617 " pdb=" CB ASP D 617 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1320 not shown) Planarity restraints: 1112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A F 17 " 0.079 2.00e-02 2.50e+03 3.21e-02 2.83e+01 pdb=" N9 A F 17 " -0.042 2.00e-02 2.50e+03 pdb=" C8 A F 17 " -0.024 2.00e-02 2.50e+03 pdb=" N7 A F 17 " -0.011 2.00e-02 2.50e+03 pdb=" C5 A F 17 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A F 17 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A F 17 " 0.045 2.00e-02 2.50e+03 pdb=" N1 A F 17 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A F 17 " -0.013 2.00e-02 2.50e+03 pdb=" N3 A F 17 " -0.016 2.00e-02 2.50e+03 pdb=" C4 A F 17 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C F 1 " -0.059 2.00e-02 2.50e+03 2.80e-02 1.77e+01 pdb=" N1 C F 1 " 0.036 2.00e-02 2.50e+03 pdb=" C2 C F 1 " 0.012 2.00e-02 2.50e+03 pdb=" O2 C F 1 " 0.009 2.00e-02 2.50e+03 pdb=" N3 C F 1 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C F 1 " 0.008 2.00e-02 2.50e+03 pdb=" N4 C F 1 " -0.039 2.00e-02 2.50e+03 pdb=" C5 C F 1 " 0.010 2.00e-02 2.50e+03 pdb=" C6 C F 1 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U F 11 " -0.055 2.00e-02 2.50e+03 2.55e-02 1.46e+01 pdb=" N1 U F 11 " 0.040 2.00e-02 2.50e+03 pdb=" C2 U F 11 " 0.006 2.00e-02 2.50e+03 pdb=" O2 U F 11 " 0.016 2.00e-02 2.50e+03 pdb=" N3 U F 11 " -0.006 2.00e-02 2.50e+03 pdb=" C4 U F 11 " -0.007 2.00e-02 2.50e+03 pdb=" O4 U F 11 " -0.021 2.00e-02 2.50e+03 pdb=" C5 U F 11 " 0.009 2.00e-02 2.50e+03 pdb=" C6 U F 11 " 0.019 2.00e-02 2.50e+03 ... (remaining 1109 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 460 2.72 - 3.27: 7668 3.27 - 3.81: 13304 3.81 - 4.36: 15846 4.36 - 4.90: 25233 Nonbonded interactions: 62511 Sorted by model distance: nonbonded pdb=" O ASP D 589 " pdb=" OG SER D 592 " model vdw 2.176 3.040 nonbonded pdb=" O2' C E 36 " pdb=" OP1 A E 38 " model vdw 2.273 3.040 nonbonded pdb=" N GLU D 116 " pdb=" OE1 GLU D 116 " model vdw 2.361 3.120 nonbonded pdb=" O GLU A 696 " pdb=" OG1 THR A 700 " model vdw 2.374 3.040 nonbonded pdb=" O ASN D 566 " pdb=" OD1 ASN D 566 " model vdw 2.376 3.040 ... (remaining 62506 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 695 through 699 or (resid 700 through 701 and (name N or n \ ame CA or name C or name O or name CB )) or resid 702 through 747)) selection = (chain 'B' and (resid 695 through 700 or (resid 701 and (name N or name CA or na \ me C or name O or name CB )) or resid 702 through 747)) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.160 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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 : 0.004 0.067 7976 Z= 0.337 Angle : 0.699 15.955 11141 Z= 0.660 Chirality : 0.046 0.803 1323 Planarity : 0.004 0.032 1112 Dihedral : 18.971 175.872 3543 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.32 % Allowed : 17.56 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.86 (0.32), residues: 706 helix: 2.08 (0.24), residues: 448 sheet: 0.52 (1.12), residues: 26 loop : -0.34 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 126 TYR 0.008 0.001 TYR D 103 PHE 0.014 0.001 PHE C 104 TRP 0.002 0.001 TRP D 522 HIS 0.009 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.34 ( 7976) covalent geometry : angle 0.69881 / 0.66 (11141) hydrogen bonds : bond 0.11228 / 7.86 ( 446) hydrogen bonds : angle 5.16427 / 3.73 ( 1214) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 740 MET cc_start: 0.8297 (tmm) cc_final: 0.7975 (tmm) REVERT: A 742 MET cc_start: 0.6777 (tmm) cc_final: 0.6549 (tmm) REVERT: A 745 GLU cc_start: 0.5309 (tt0) cc_final: 0.5105 (tm-30) REVERT: D 617 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8380 (t70) REVERT: D 768 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8148 (tm-30) REVERT: C 44 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8370 (mmmt) outliers start: 2 outliers final: 0 residues processed: 122 average time/residue: 0.1038 time to fit residues: 16.6512 Evaluate side-chains 103 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 617 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.0270 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.0000 chunk 74 optimal weight: 10.0000 overall best weight: 0.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 721 GLN D 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.149977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.112505 restraints weight = 13773.217| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.42 r_work: 0.3406 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7976 Z= 0.135 Angle : 0.517 5.816 11141 Z= 0.307 Chirality : 0.037 0.359 1323 Planarity : 0.004 0.033 1112 Dihedral : 16.523 165.386 2055 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.27 % Allowed : 18.20 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.92 (0.31), residues: 706 helix: 2.11 (0.24), residues: 455 sheet: 0.13 (1.02), residues: 27 loop : -0.30 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 736 TYR 0.008 0.001 TYR D 103 PHE 0.034 0.002 PHE C 104 TRP 0.003 0.001 TRP D 692 HIS 0.005 0.001 HIS D 616 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 7976) covalent geometry : angle 0.51704 / 0.31 (11141) hydrogen bonds : bond 0.04868 / 3.30 ( 446) hydrogen bonds : angle 4.29212 / 3.12 ( 1214) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 745 GLU cc_start: 0.5207 (tt0) cc_final: 0.4944 (tm-30) REVERT: B 743 ASP cc_start: 0.6584 (t70) cc_final: 0.6378 (t70) REVERT: D 12 MET cc_start: 0.8670 (mmm) cc_final: 0.8423 (mmm) REVERT: D 768 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8314 (tm-30) REVERT: C 19 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8029 (mt-10) outliers start: 8 outliers final: 5 residues processed: 112 average time/residue: 0.1073 time to fit residues: 15.7856 Evaluate side-chains 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 537 LYS Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 163 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 0.0570 chunk 15 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.150213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.112580 restraints weight = 13749.874| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.44 r_work: 0.3401 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7976 Z= 0.122 Angle : 0.488 7.459 11141 Z= 0.282 Chirality : 0.037 0.368 1323 Planarity : 0.004 0.037 1112 Dihedral : 16.533 171.235 2053 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.69 % Allowed : 18.51 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.96 (0.31), residues: 706 helix: 2.14 (0.24), residues: 460 sheet: 0.30 (0.96), residues: 25 loop : -0.38 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 699 TYR 0.019 0.001 TYR D 393 PHE 0.025 0.002 PHE C 104 TRP 0.003 0.001 TRP D 692 HIS 0.003 0.001 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 7976) covalent geometry : angle 0.48778 / 0.28 (11141) hydrogen bonds : bond 0.04398 / 2.96 ( 446) hydrogen bonds : angle 4.10474 / 3.01 ( 1214) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 745 GLU cc_start: 0.5150 (tt0) cc_final: 0.4917 (tm-30) REVERT: D 12 MET cc_start: 0.8697 (mmm) cc_final: 0.8460 (mmm) REVERT: D 748 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.8049 (m-40) REVERT: D 768 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8354 (tm-30) outliers start: 17 outliers final: 10 residues processed: 115 average time/residue: 0.1031 time to fit residues: 15.8093 Evaluate side-chains 112 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain D residue 537 LYS Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 713 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 748 ASN Chi-restraints excluded: chain D residue 813 MET Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 163 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 0.0670 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.150111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.112186 restraints weight = 13942.952| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.46 r_work: 0.3400 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7976 Z= 0.118 Angle : 0.461 7.729 11141 Z= 0.267 Chirality : 0.036 0.337 1323 Planarity : 0.003 0.035 1112 Dihedral : 16.496 169.285 2053 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.85 % Allowed : 19.62 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.94 (0.31), residues: 706 helix: 2.12 (0.24), residues: 460 sheet: 0.07 (0.96), residues: 25 loop : -0.34 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 699 TYR 0.009 0.001 TYR D 103 PHE 0.036 0.002 PHE C 104 TRP 0.004 0.001 TRP D 522 HIS 0.003 0.000 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 7976) covalent geometry : angle 0.46069 / 0.27 (11141) hydrogen bonds : bond 0.04197 / 2.83 ( 446) hydrogen bonds : angle 3.99086 / 2.93 ( 1214) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 745 GLU cc_start: 0.5162 (tt0) cc_final: 0.4757 (tm-30) REVERT: B 737 LEU cc_start: 0.8326 (tp) cc_final: 0.8123 (tp) REVERT: D 12 MET cc_start: 0.8688 (mmm) cc_final: 0.8451 (mmm) REVERT: D 748 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.8087 (m-40) REVERT: D 768 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8351 (tm-30) outliers start: 18 outliers final: 13 residues processed: 120 average time/residue: 0.1031 time to fit residues: 16.4641 Evaluate side-chains 115 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain D residue 537 LYS Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 713 ILE Chi-restraints excluded: chain D residue 718 PHE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 748 ASN Chi-restraints excluded: chain D residue 813 MET Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 163 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 44 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.148609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.113614 restraints weight = 13931.307| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.14 r_work: 0.3417 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7976 Z= 0.115 Angle : 0.465 9.042 11141 Z= 0.267 Chirality : 0.035 0.326 1323 Planarity : 0.003 0.033 1112 Dihedral : 16.507 173.275 2053 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.01 % Allowed : 19.94 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.99 (0.31), residues: 706 helix: 2.14 (0.23), residues: 459 sheet: -0.00 (0.96), residues: 25 loop : -0.24 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 699 TYR 0.009 0.001 TYR D 103 PHE 0.025 0.002 PHE C 104 TRP 0.003 0.001 TRP D 522 HIS 0.003 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 7976) covalent geometry : angle 0.46506 / 0.27 (11141) hydrogen bonds : bond 0.04080 / 2.74 ( 446) hydrogen bonds : angle 3.91989 / 2.89 ( 1214) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 706 ASN cc_start: 0.8203 (t0) cc_final: 0.7995 (t0) REVERT: A 745 GLU cc_start: 0.5017 (tt0) cc_final: 0.4640 (tm-30) REVERT: D 12 MET cc_start: 0.8538 (mmm) cc_final: 0.8306 (mmm) REVERT: D 386 GLU cc_start: 0.5249 (tp30) cc_final: 0.4920 (tp30) REVERT: D 748 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.8038 (m-40) REVERT: D 768 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8294 (tm-30) REVERT: C 45 GLU cc_start: 0.7400 (tp30) cc_final: 0.7163 (tp30) outliers start: 19 outliers final: 11 residues processed: 120 average time/residue: 0.1005 time to fit residues: 16.0914 Evaluate side-chains 112 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain D residue 537 LYS Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 713 ILE Chi-restraints excluded: chain D residue 718 PHE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 748 ASN Chi-restraints excluded: chain D residue 813 MET Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 163 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 53 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 728 GLN ** D 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.144453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.107346 restraints weight = 14065.243| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.35 r_work: 0.3346 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7976 Z= 0.234 Angle : 0.559 8.886 11141 Z= 0.314 Chirality : 0.040 0.327 1323 Planarity : 0.004 0.036 1112 Dihedral : 16.535 172.914 2053 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.59 % Allowed : 20.09 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.77 (0.31), residues: 706 helix: 2.02 (0.24), residues: 455 sheet: -0.05 (0.98), residues: 25 loop : -0.41 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 699 TYR 0.015 0.002 TYR D 103 PHE 0.024 0.003 PHE C 17 TRP 0.010 0.002 TRP D 692 HIS 0.004 0.001 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 ( 7976) covalent geometry : angle 0.55868 / 0.31 (11141) hydrogen bonds : bond 0.05218 / 3.47 ( 446) hydrogen bonds : angle 4.22402 / 3.13 ( 1214) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 745 GLU cc_start: 0.5102 (tt0) cc_final: 0.4693 (tm-30) REVERT: D 748 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.7982 (m-40) REVERT: D 768 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8314 (tm-30) REVERT: C 123 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7416 (mm) outliers start: 29 outliers final: 22 residues processed: 122 average time/residue: 0.0989 time to fit residues: 16.1696 Evaluate side-chains 124 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 537 LYS Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 577 GLU Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 713 ILE Chi-restraints excluded: chain D residue 718 PHE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 748 ASN Chi-restraints excluded: chain D residue 813 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 163 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 22 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 608 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.148173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.110197 restraints weight = 13941.665| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.37 r_work: 0.3389 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7976 Z= 0.122 Angle : 0.493 10.285 11141 Z= 0.279 Chirality : 0.036 0.324 1323 Planarity : 0.003 0.035 1112 Dihedral : 16.660 173.634 2053 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.48 % Allowed : 21.68 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.91 (0.31), residues: 706 helix: 2.10 (0.24), residues: 457 sheet: -0.29 (0.95), residues: 25 loop : -0.29 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 699 TYR 0.009 0.001 TYR D 103 PHE 0.041 0.002 PHE C 104 TRP 0.004 0.001 TRP D 522 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 7976) covalent geometry : angle 0.49270 / 0.28 (11141) hydrogen bonds : bond 0.04278 / 2.84 ( 446) hydrogen bonds : angle 3.97213 / 2.94 ( 1214) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 745 GLU cc_start: 0.5022 (tt0) cc_final: 0.4634 (tm-30) REVERT: B 747 ARG cc_start: 0.6332 (ttm170) cc_final: 0.6065 (mtm180) REVERT: D 596 MET cc_start: 0.8422 (ttm) cc_final: 0.8187 (mtt) REVERT: D 748 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7987 (m-40) REVERT: D 768 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8321 (tm-30) REVERT: C 123 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7360 (mm) outliers start: 22 outliers final: 13 residues processed: 120 average time/residue: 0.0864 time to fit residues: 13.9556 Evaluate side-chains 115 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain D residue 537 LYS Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 713 ILE Chi-restraints excluded: chain D residue 718 PHE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 748 ASN Chi-restraints excluded: chain D residue 813 MET Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 163 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 78 optimal weight: 20.0000 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 701 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.148428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.112013 restraints weight = 13938.717| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.33 r_work: 0.3410 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7976 Z= 0.118 Angle : 0.503 14.503 11141 Z= 0.279 Chirality : 0.035 0.318 1323 Planarity : 0.004 0.034 1112 Dihedral : 16.634 173.353 2053 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.85 % Allowed : 22.63 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.85 (0.31), residues: 706 helix: 2.05 (0.24), residues: 460 sheet: -0.51 (0.92), residues: 25 loop : -0.27 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 699 TYR 0.013 0.001 TYR C 103 PHE 0.029 0.002 PHE C 104 TRP 0.004 0.001 TRP D 522 HIS 0.002 0.001 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 7976) covalent geometry : angle 0.50336 / 0.28 (11141) hydrogen bonds : bond 0.04216 / 2.80 ( 446) hydrogen bonds : angle 3.88779 / 2.88 ( 1214) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 745 GLU cc_start: 0.5098 (tt0) cc_final: 0.4674 (tm-30) REVERT: B 747 ARG cc_start: 0.6235 (ttm170) cc_final: 0.5962 (mtm180) REVERT: D 12 MET cc_start: 0.8540 (mmm) cc_final: 0.8296 (mmm) REVERT: D 596 MET cc_start: 0.8413 (ttm) cc_final: 0.8166 (mtt) REVERT: D 768 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8271 (tm-30) outliers start: 18 outliers final: 14 residues processed: 116 average time/residue: 0.0830 time to fit residues: 12.9034 Evaluate side-chains 116 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain D residue 537 LYS Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 713 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 813 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 163 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 69 optimal weight: 0.9990 chunk 58 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 701 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.148594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.112284 restraints weight = 13911.361| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.32 r_work: 0.3408 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7976 Z= 0.121 Angle : 0.515 15.154 11141 Z= 0.281 Chirality : 0.037 0.320 1323 Planarity : 0.003 0.034 1112 Dihedral : 16.627 172.190 2053 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.69 % Allowed : 23.73 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.93 (0.31), residues: 706 helix: 2.13 (0.24), residues: 459 sheet: -0.63 (0.89), residues: 25 loop : -0.27 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 699 TYR 0.010 0.001 TYR C 103 PHE 0.026 0.002 PHE C 104 TRP 0.008 0.001 TRP D 522 HIS 0.003 0.000 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 7976) covalent geometry : angle 0.51463 / 0.28 (11141) hydrogen bonds : bond 0.04101 / 2.72 ( 446) hydrogen bonds : angle 3.87053 / 2.86 ( 1214) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.233 Fit side-chains REVERT: A 745 GLU cc_start: 0.5134 (tt0) cc_final: 0.4729 (tm-30) REVERT: B 747 ARG cc_start: 0.6261 (ttm170) cc_final: 0.6016 (mtm180) REVERT: D 12 MET cc_start: 0.8554 (mmm) cc_final: 0.8326 (mmm) REVERT: D 596 MET cc_start: 0.8376 (ttm) cc_final: 0.8148 (mtt) REVERT: D 679 ASP cc_start: 0.7299 (t0) cc_final: 0.7002 (t70) REVERT: D 768 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8323 (tm-30) REVERT: C 45 GLU cc_start: 0.7377 (tp30) cc_final: 0.7144 (tp30) outliers start: 17 outliers final: 14 residues processed: 112 average time/residue: 0.0935 time to fit residues: 13.9762 Evaluate side-chains 117 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 537 LYS Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 813 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 163 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 19 optimal weight: 0.7980 chunk 78 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 44 optimal weight: 0.0030 chunk 65 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 0.0670 chunk 42 optimal weight: 1.9990 overall best weight: 0.3928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 701 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.150876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.113096 restraints weight = 13847.401| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.44 r_work: 0.3429 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7976 Z= 0.107 Angle : 0.508 15.148 11141 Z= 0.275 Chirality : 0.035 0.320 1323 Planarity : 0.003 0.032 1112 Dihedral : 16.621 168.651 2053 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.74 % Allowed : 25.00 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.93 (0.31), residues: 706 helix: 2.14 (0.24), residues: 460 sheet: -0.66 (0.88), residues: 25 loop : -0.29 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG D 699 TYR 0.010 0.001 TYR D 549 PHE 0.021 0.001 PHE C 104 TRP 0.005 0.001 TRP D 522 HIS 0.002 0.000 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 ( 7976) covalent geometry : angle 0.50797 / 0.27 (11141) hydrogen bonds : bond 0.03870 / 2.58 ( 446) hydrogen bonds : angle 3.78395 / 2.79 ( 1214) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.274 Fit side-chains REVERT: A 745 GLU cc_start: 0.5110 (tt0) cc_final: 0.4737 (tm-30) REVERT: B 747 ARG cc_start: 0.6172 (ttm170) cc_final: 0.5943 (mtm180) REVERT: D 12 MET cc_start: 0.8568 (mmm) cc_final: 0.8351 (mmm) REVERT: D 548 LYS cc_start: 0.8773 (ttpt) cc_final: 0.8466 (tmmt) REVERT: D 596 MET cc_start: 0.8361 (ttm) cc_final: 0.8094 (mtt) REVERT: D 679 ASP cc_start: 0.7316 (t0) cc_final: 0.7015 (t70) REVERT: D 748 ASN cc_start: 0.8243 (p0) cc_final: 0.8018 (m-40) REVERT: D 768 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8339 (tm-30) REVERT: C 45 GLU cc_start: 0.7405 (tp30) cc_final: 0.7151 (tp30) outliers start: 11 outliers final: 9 residues processed: 112 average time/residue: 0.0877 time to fit residues: 13.4234 Evaluate side-chains 114 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain D residue 537 LYS Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 813 MET Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 163 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.0020 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 0.0070 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 overall best weight: 0.4808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 701 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.151183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.114306 restraints weight = 13759.666| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.39 r_work: 0.3437 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7976 Z= 0.109 Angle : 0.512 15.984 11141 Z= 0.276 Chirality : 0.035 0.319 1323 Planarity : 0.003 0.034 1112 Dihedral : 16.563 164.868 2053 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.74 % Allowed : 25.00 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.08 (0.31), residues: 706 helix: 2.25 (0.24), residues: 459 sheet: -0.68 (0.89), residues: 25 loop : -0.20 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 699 TYR 0.008 0.001 TYR C 103 PHE 0.021 0.001 PHE C 104 TRP 0.008 0.001 TRP D 522 HIS 0.002 0.000 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 7976) covalent geometry : angle 0.51192 / 0.28 (11141) hydrogen bonds : bond 0.03856 / 2.57 ( 446) hydrogen bonds : angle 3.79043 / 2.79 ( 1214) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1924.92 seconds wall clock time: 33 minutes 49.13 seconds (2029.13 seconds total)