Starting phenix.real_space_refine on Sun Apr 5 03:18:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rvz_54293/04_2026/9rvz_54293.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rvz_54293/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9rvz_54293/04_2026/9rvz_54293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rvz_54293/04_2026/9rvz_54293.map" model { file = "/net/cci-nas-00/data/ceres_data/9rvz_54293/04_2026/9rvz_54293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rvz_54293/04_2026/9rvz_54293.cif" } 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-2.1rc1-6017/lib/python3.9/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: 1.82, per 1000 atoms: 0.24 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: 0.85 Conformation dependent library (CDL) restraints added in 202.2 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: 1.16 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: 1.43 Time building geometry restraints manager: 1.07 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=" 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=" O4' C E 33 " pdb=" C4' C E 33 " pdb=" C3' C E 33 " ideal model delta sigma weight residual 106.10 100.72 5.38 1.00e+00 1.00e+00 2.89e+01 angle pdb=" C4' A F 10 " pdb=" C3' A F 10 " pdb=" O3' A F 10 " ideal model delta sigma weight residual 113.00 106.84 6.16 1.50e+00 4.44e-01 1.69e+01 angle pdb=" CA VAL D 75 " pdb=" C VAL D 75 " pdb=" O VAL D 75 " ideal model delta sigma weight residual 120.67 116.46 4.21 1.12e+00 7.97e-01 1.41e+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: 1.120 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 9.930 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: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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= 0.245 Angle : 0.699 15.955 11141 Z= 0.394 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 covalent geometry : bond 0.00414 ( 7976) covalent geometry : angle 0.69878 (11141) hydrogen bonds : bond 0.11228 ( 446) hydrogen bonds : angle 5.16427 ( 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 : 0.274 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: 0.1008 time to fit residues: 15.8758 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 : 0.258 ------------------------------------------------------------------------------- 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: 6.9990 overall best weight: 0.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4121 r_free = 0.4121 target = 0.151488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.114032 restraints weight = 13867.251| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.47 r_work: 0.3430 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7976 Z= 0.112 Angle : 0.505 6.846 11141 Z= 0.271 Chirality : 0.035 0.328 1323 Planarity : 0.003 0.034 1112 Dihedral : 16.532 169.525 2055 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.22 % Allowed : 18.04 % Favored : 79.75 % 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: 2.19 (0.31), residues: 706 helix: 2.31 (0.24), residues: 456 sheet: 0.23 (1.02), residues: 27 loop : -0.20 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 736 TYR 0.010 0.001 TYR D 704 PHE 0.025 0.002 PHE C 104 TRP 0.001 0.000 TRP D 692 HIS 0.002 0.000 HIS D 643 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 7976) covalent geometry : angle 0.50519 (11141) hydrogen bonds : bond 0.03829 ( 446) hydrogen bonds : angle 4.06770 ( 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 139 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 738 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7418 (tm-30) REVERT: A 745 GLU cc_start: 0.5150 (tt0) cc_final: 0.4734 (tm-30) REVERT: D 12 MET cc_start: 0.8733 (mmm) cc_final: 0.8470 (mmm) REVERT: C 19 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8013 (mt-10) REVERT: C 45 GLU cc_start: 0.7475 (tp30) cc_final: 0.7272 (tp30) outliers start: 14 outliers final: 8 residues processed: 131 average time/residue: 0.1013 time to fit residues: 17.4972 Evaluate side-chains 111 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain B residue 702 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 137 SER 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: 0.9990 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.149206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.112825 restraints weight = 13829.827| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.33 r_work: 0.3419 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7976 Z= 0.114 Angle : 0.481 9.205 11141 Z= 0.255 Chirality : 0.034 0.316 1323 Planarity : 0.003 0.035 1112 Dihedral : 16.458 175.265 2053 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.85 % Allowed : 18.51 % Favored : 78.64 % 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: 2.23 (0.31), residues: 706 helix: 2.33 (0.24), residues: 459 sheet: -0.09 (0.99), residues: 27 loop : -0.13 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 699 TYR 0.010 0.001 TYR D 103 PHE 0.017 0.002 PHE C 104 TRP 0.003 0.001 TRP D 522 HIS 0.005 0.001 HIS C 151 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 7976) covalent geometry : angle 0.48073 (11141) hydrogen bonds : bond 0.03717 ( 446) hydrogen bonds : angle 3.89075 ( 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 134 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 745 GLU cc_start: 0.5113 (tt0) cc_final: 0.4724 (tm-30) REVERT: D 12 MET cc_start: 0.8567 (mmm) cc_final: 0.8324 (mmm) REVERT: D 701 MET cc_start: 0.5468 (mtm) cc_final: 0.5251 (mtm) outliers start: 18 outliers final: 10 residues processed: 124 average time/residue: 0.0961 time to fit residues: 15.9165 Evaluate side-chains 110 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 597 VAL 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 813 MET Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 117 VAL 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: 1.9990 chunk 20 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 0.0570 chunk 43 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 701 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.150459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.112519 restraints weight = 13794.380| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.40 r_work: 0.3395 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7976 Z= 0.130 Angle : 0.490 8.826 11141 Z= 0.261 Chirality : 0.034 0.323 1323 Planarity : 0.003 0.036 1112 Dihedral : 16.495 173.309 2053 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.69 % Allowed : 18.83 % Favored : 78.48 % 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: 2.19 (0.31), residues: 706 helix: 2.31 (0.24), residues: 458 sheet: -0.36 (0.99), residues: 27 loop : -0.11 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 699 TYR 0.010 0.001 TYR D 103 PHE 0.018 0.002 PHE C 104 TRP 0.003 0.001 TRP D 522 HIS 0.003 0.000 HIS D 643 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7976) covalent geometry : angle 0.49021 (11141) hydrogen bonds : bond 0.03865 ( 446) hydrogen bonds : angle 3.83373 ( 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 126 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 745 GLU cc_start: 0.5137 (tt0) cc_final: 0.4760 (tm-30) REVERT: D 12 MET cc_start: 0.8688 (mmm) cc_final: 0.8433 (mmm) REVERT: D 701 MET cc_start: 0.5649 (mtm) cc_final: 0.5426 (mtm) REVERT: D 768 GLN cc_start: 0.8692 (tm-30) cc_final: 0.8378 (tm-30) REVERT: C 45 GLU cc_start: 0.7545 (tp30) cc_final: 0.7310 (tp30) outliers start: 17 outliers final: 12 residues processed: 116 average time/residue: 0.0999 time to fit residues: 15.3743 Evaluate side-chains 115 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain D residue 577 GLU Chi-restraints excluded: chain D residue 597 VAL 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 813 MET Chi-restraints excluded: chain C residue 101 LYS 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: 1.9990 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 701 GLN D 608 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.150574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.113526 restraints weight = 13755.741| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.39 r_work: 0.3413 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7976 Z= 0.115 Angle : 0.483 8.703 11141 Z= 0.253 Chirality : 0.034 0.320 1323 Planarity : 0.003 0.034 1112 Dihedral : 16.477 164.878 2053 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.22 % Allowed : 20.25 % 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: 2.25 (0.31), residues: 706 helix: 2.34 (0.24), residues: 459 sheet: -0.49 (0.99), residues: 27 loop : -0.06 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 699 TYR 0.009 0.001 TYR D 103 PHE 0.015 0.002 PHE C 104 TRP 0.003 0.001 TRP D 522 HIS 0.002 0.000 HIS D 643 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 7976) covalent geometry : angle 0.48345 (11141) hydrogen bonds : bond 0.03700 ( 446) hydrogen bonds : angle 3.72281 ( 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 124 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 745 GLU cc_start: 0.5007 (tt0) cc_final: 0.4652 (tm-30) REVERT: B 737 LEU cc_start: 0.8353 (tp) cc_final: 0.8056 (tp) REVERT: D 12 MET cc_start: 0.8583 (mmm) cc_final: 0.8350 (mmm) REVERT: D 768 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8325 (tm-30) REVERT: C 45 GLU cc_start: 0.7614 (tp30) cc_final: 0.7384 (tp30) outliers start: 14 outliers final: 13 residues processed: 116 average time/residue: 0.0938 time to fit residues: 14.4658 Evaluate side-chains 115 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 577 GLU Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 698 THR 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 813 MET Chi-restraints excluded: chain C residue 101 LYS 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: 1.9990 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 701 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.147864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.111256 restraints weight = 13955.675| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.23 r_work: 0.3349 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7976 Z= 0.173 Angle : 0.529 6.986 11141 Z= 0.278 Chirality : 0.035 0.239 1323 Planarity : 0.003 0.036 1112 Dihedral : 16.462 159.185 2053 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.16 % Allowed : 20.89 % Favored : 75.95 % 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: 2.02 (0.31), residues: 706 helix: 2.12 (0.24), residues: 463 sheet: -0.56 (1.04), residues: 27 loop : -0.08 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 699 TYR 0.011 0.001 TYR D 103 PHE 0.020 0.002 PHE C 144 TRP 0.008 0.002 TRP D 692 HIS 0.002 0.001 HIS C 151 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 7976) covalent geometry : angle 0.52947 (11141) hydrogen bonds : bond 0.04359 ( 446) hydrogen bonds : angle 3.92709 ( 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 131 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 745 GLU cc_start: 0.5208 (tt0) cc_final: 0.4785 (tm-30) REVERT: B 737 LEU cc_start: 0.8408 (tp) cc_final: 0.8111 (tp) REVERT: D 768 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8363 (tm-30) REVERT: C 45 GLU cc_start: 0.7685 (tp30) cc_final: 0.7444 (tp30) outliers start: 20 outliers final: 15 residues processed: 119 average time/residue: 0.0968 time to fit residues: 15.2163 Evaluate side-chains 120 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 734 THR 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 698 THR 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 813 MET Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 117 VAL 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: 10.0000 chunk 49 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 66 optimal weight: 0.0570 chunk 5 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 701 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.151123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.115157 restraints weight = 13821.537| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.30 r_work: 0.3407 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7976 Z= 0.105 Angle : 0.488 7.459 11141 Z= 0.254 Chirality : 0.033 0.181 1323 Planarity : 0.003 0.035 1112 Dihedral : 16.447 159.773 2053 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.37 % Allowed : 21.68 % Favored : 75.95 % 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: 2.11 (0.31), residues: 706 helix: 2.22 (0.24), residues: 460 sheet: -0.68 (0.99), residues: 27 loop : -0.07 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 699 TYR 0.008 0.001 TYR D 103 PHE 0.017 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 covalent geometry : bond 0.00228 ( 7976) covalent geometry : angle 0.48769 (11141) hydrogen bonds : bond 0.03654 ( 446) hydrogen bonds : angle 3.70533 ( 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 129 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 745 GLU cc_start: 0.5123 (tt0) cc_final: 0.4747 (tm-30) REVERT: B 701 GLN cc_start: 0.7871 (tm130) cc_final: 0.7623 (tp40) REVERT: D 12 MET cc_start: 0.8702 (mmm) cc_final: 0.8477 (mmm) REVERT: D 527 LEU cc_start: 0.8300 (mt) cc_final: 0.8065 (mt) REVERT: D 768 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8367 (tm-30) REVERT: C 45 GLU cc_start: 0.7689 (tp30) cc_final: 0.7423 (tp30) outliers start: 15 outliers final: 10 residues processed: 119 average time/residue: 0.0983 time to fit residues: 15.6027 Evaluate side-chains 114 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 565 ILE Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 698 THR Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 813 MET Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 117 VAL 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: 0.5980 chunk 65 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.150321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.114121 restraints weight = 13916.242| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.30 r_work: 0.3388 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2720 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= 0.119 Angle : 0.504 8.272 11141 Z= 0.262 Chirality : 0.033 0.175 1323 Planarity : 0.003 0.034 1112 Dihedral : 16.395 159.651 2053 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.06 % Allowed : 23.26 % Favored : 74.68 % 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: 2.01 (0.24), residues: 474 sheet: -0.69 (1.01), residues: 27 loop : -0.08 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 699 TYR 0.009 0.001 TYR D 103 PHE 0.026 0.002 PHE C 104 TRP 0.006 0.001 TRP D 522 HIS 0.002 0.000 HIS D 643 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7976) covalent geometry : angle 0.50427 (11141) hydrogen bonds : bond 0.03760 ( 446) hydrogen bonds : angle 3.73168 ( 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 125 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 745 GLU cc_start: 0.5024 (tt0) cc_final: 0.4651 (tm-30) REVERT: D 12 MET cc_start: 0.8696 (mmm) cc_final: 0.8465 (mmm) REVERT: D 768 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8386 (tm-30) REVERT: C 45 GLU cc_start: 0.7681 (tp30) cc_final: 0.7419 (tp30) outliers start: 13 outliers final: 10 residues processed: 116 average time/residue: 0.0999 time to fit residues: 15.5271 Evaluate side-chains 117 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 565 ILE Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 698 THR Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 813 MET Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 117 VAL 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: 1.9990 chunk 58 optimal weight: 0.0070 chunk 23 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.150590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.114684 restraints weight = 13905.380| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.26 r_work: 0.3399 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7976 Z= 0.117 Angle : 0.509 8.684 11141 Z= 0.263 Chirality : 0.033 0.169 1323 Planarity : 0.003 0.035 1112 Dihedral : 16.404 159.611 2053 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.74 % Allowed : 22.78 % Favored : 75.47 % 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: 2.04 (0.31), residues: 706 helix: 2.09 (0.24), residues: 467 sheet: -0.71 (1.00), residues: 27 loop : 0.03 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 699 TYR 0.009 0.001 TYR D 103 PHE 0.023 0.002 PHE C 104 TRP 0.006 0.001 TRP D 522 HIS 0.003 0.000 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7976) covalent geometry : angle 0.50894 (11141) hydrogen bonds : bond 0.03704 ( 446) hydrogen bonds : angle 3.71673 ( 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 118 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: D 12 MET cc_start: 0.8705 (mmm) cc_final: 0.8478 (mmm) REVERT: D 386 GLU cc_start: 0.5538 (tp30) cc_final: 0.5181 (tp30) REVERT: D 548 LYS cc_start: 0.8857 (tmmt) cc_final: 0.8450 (tmmt) REVERT: D 768 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8377 (tm-30) REVERT: C 45 GLU cc_start: 0.7679 (tp30) cc_final: 0.7441 (tp30) outliers start: 11 outliers final: 11 residues processed: 110 average time/residue: 0.0940 time to fit residues: 13.8680 Evaluate side-chains 115 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 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 565 ILE Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 698 THR Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 813 MET Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 117 VAL 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: 10.0000 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.145395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.108189 restraints weight = 13773.972| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.35 r_work: 0.3290 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7976 Z= 0.192 Angle : 0.583 8.132 11141 Z= 0.301 Chirality : 0.036 0.172 1323 Planarity : 0.004 0.038 1112 Dihedral : 16.547 159.069 2053 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.12 % Favored : 96.74 % Rotamer: Outliers : 2.06 % Allowed : 22.63 % 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: 1.78 (0.31), residues: 706 helix: 1.93 (0.24), residues: 464 sheet: -0.80 (1.04), residues: 27 loop : -0.16 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 699 TYR 0.013 0.001 TYR D 103 PHE 0.027 0.003 PHE C 104 TRP 0.011 0.002 TRP D 692 HIS 0.002 0.001 HIS D 643 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 7976) covalent geometry : angle 0.58252 (11141) hydrogen bonds : bond 0.04524 ( 446) hydrogen bonds : angle 3.98890 ( 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 111 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 745 GLU cc_start: 0.5287 (tt0) cc_final: 0.4797 (tm-30) REVERT: B 737 LEU cc_start: 0.8502 (tp) cc_final: 0.8265 (tp) REVERT: D 768 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8400 (tm-30) REVERT: C 45 GLU cc_start: 0.7760 (tp30) cc_final: 0.7519 (tp30) outliers start: 13 outliers final: 13 residues processed: 103 average time/residue: 0.0987 time to fit residues: 13.6253 Evaluate side-chains 110 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 565 ILE Chi-restraints excluded: chain D residue 577 GLU Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 698 THR 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 813 MET Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 117 VAL 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: 1.9990 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.149751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.113892 restraints weight = 13761.930| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.22 r_work: 0.3387 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7976 Z= 0.124 Angle : 0.530 7.923 11141 Z= 0.272 Chirality : 0.033 0.158 1323 Planarity : 0.003 0.037 1112 Dihedral : 16.559 159.641 2053 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.90 % Allowed : 23.10 % Favored : 75.00 % 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: 1.89 (0.31), residues: 706 helix: 2.03 (0.24), residues: 467 sheet: -0.80 (1.03), residues: 27 loop : -0.16 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 699 TYR 0.008 0.001 TYR D 103 PHE 0.023 0.002 PHE C 104 TRP 0.007 0.001 TRP D 522 HIS 0.002 0.001 HIS D 643 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7976) covalent geometry : angle 0.52984 (11141) hydrogen bonds : bond 0.03869 ( 446) hydrogen bonds : angle 3.79765 ( 1214) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1986.99 seconds wall clock time: 34 minutes 46.61 seconds (2086.61 seconds total)