Starting phenix.real_space_refine on Wed Aug 5 01:26:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rw7_54302/08_2026/9rw7_54302.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rw7_54302/08_2026/9rw7_54302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rw7_54302/08_2026/9rw7_54302.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rw7_54302/08_2026/9rw7_54302.map" model { file = "/net/cci-nas-00/data/ceres_data/9rw7_54302/08_2026/9rw7_54302.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rw7_54302/08_2026/9rw7_54302.cif" } resolution = 3.4 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= 0.054 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 98 5.49 5 S 38 5.16 5 C 4561 2.51 5 N 1342 2.21 5 O 1777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7816 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 423 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 423 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 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: "D" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3623 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 448} Chain breaks: 3 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "E" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1049 Classifications: {'RNA': 50} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 7, 'rna3p_pur': 21, 'rna3p_pyr': 21} Link IDs: {'rna2p': 8, 'rna3p': 41} Chain breaks: 1 Chain: "F" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1049 Classifications: {'RNA': 50} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 7, 'rna3p_pur': 21, 'rna3p_pyr': 21} Link IDs: {'rna2p': 8, 'rna3p': 41} Chain breaks: 1 Time building chain proxies: 1.61, per 1000 atoms: 0.21 Number of scatterers: 7816 At special positions: 0 Unit cell: (90.015, 97.428, 150.378, 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 98 15.00 O 1777 8.00 N 1342 7.00 C 4561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 358.3 milliseconds 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1372 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 5 sheets defined 69.9% alpha, 7.5% beta 42 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 695 through 747 removed outlier: 3.605A 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 'C' and resid 6 through 25 removed outlier: 3.627A pdb=" N LYS C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 36 through 39 Processing helix chain 'C' and resid 43 through 51 removed outlier: 3.596A pdb=" N GLY C 51 " --> pdb=" O ARG C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 62 Processing helix chain 'C' and resid 95 through 110 Processing helix chain 'C' and resid 119 through 125 removed outlier: 3.679A pdb=" N GLY C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HIS C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 128 No H-bonds generated for 'chain 'C' and resid 126 through 128' Processing helix chain 'C' and resid 130 through 137 Processing helix chain 'C' and resid 140 through 150 Processing helix chain 'D' and resid 5 through 25 removed outlier: 3.831A pdb=" N LYS D 24 " --> pdb=" O ARG D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 35 Processing helix chain 'D' and resid 36 through 39 Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'D' and resid 53 through 62 Processing helix chain 'D' and resid 95 through 111 removed outlier: 3.720A pdb=" N GLU D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 123 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 130 through 137 removed outlier: 3.505A pdb=" N ILE D 136 " --> pdb=" O GLN D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 152 removed outlier: 3.787A pdb=" N HIS D 151 " --> pdb=" O PHE D 147 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 529 Processing helix chain 'D' and resid 535 through 554 Processing helix chain 'D' and resid 594 through 600 removed outlier: 4.136A 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 617 through 630 removed outlier: 4.380A pdb=" N ASP D 621 " --> pdb=" O ASP D 617 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D 625 " --> pdb=" O ASP D 621 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR D 626 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 652 Processing helix chain 'D' and resid 662 through 670 Processing helix chain 'D' and resid 675 through 680 removed outlier: 3.881A pdb=" N LYS D 678 " --> pdb=" O ASN D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 688 Processing helix chain 'D' and resid 689 through 694 removed outlier: 4.545A pdb=" N TRP D 692 " --> pdb=" O GLN D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 714 removed outlier: 4.159A pdb=" N ASP D 708 " --> pdb=" O TYR D 704 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL D 709 " --> pdb=" O ALA D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 725 Processing helix chain 'D' and resid 726 through 728 No H-bonds generated for 'chain 'D' and resid 726 through 728' Processing helix chain 'D' and resid 729 through 743 Processing helix chain 'D' and resid 746 through 773 removed outlier: 3.524A pdb=" N SER D 764 " --> pdb=" O SER D 760 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR D 773 " --> pdb=" O LYS D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 780 through 787 removed outlier: 3.510A pdb=" N ARG D 785 " --> pdb=" O ASN D 781 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU D 787 " --> pdb=" O GLU D 783 " (cutoff:3.500A) 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 sheet with id=AA1, first strand: chain 'C' and resid 28 through 29 removed outlier: 3.846A pdb=" N TYR C 74 " --> pdb=" O ASP C 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AA3, first strand: chain 'D' and resid 28 through 29 Processing sheet with id=AA4, first strand: chain 'D' and resid 117 through 118 Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 533 removed outlier: 3.524A pdb=" N ILE D 576 " --> pdb=" O PHE D 588 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ILE D 573 " --> pdb=" O ILE D 565 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE D 565 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 575 " --> pdb=" O GLU D 563 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS D 613 " --> pdb=" O PHE D 637 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 96 hydrogen bonds 176 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1105 1.31 - 1.43: 2612 1.43 - 1.56: 4162 1.56 - 1.69: 196 1.69 - 1.81: 63 Bond restraints: 8138 Sorted by residual: bond pdb=" CG PRO D 696 " pdb=" CD PRO D 696 " ideal model delta sigma weight residual 1.512 1.180 0.332 2.70e-02 1.37e+03 1.52e+02 bond pdb=" N PRO D 696 " pdb=" CD PRO D 696 " ideal model delta sigma weight residual 1.474 1.562 -0.088 1.40e-02 5.10e+03 3.96e+01 bond pdb=" N PRO D 696 " pdb=" CA PRO D 696 " ideal model delta sigma weight residual 1.468 1.383 0.085 1.70e-02 3.46e+03 2.53e+01 bond pdb=" C HIS C 31 " pdb=" O HIS C 31 " ideal model delta sigma weight residual 1.237 1.186 0.051 1.17e-02 7.31e+03 1.88e+01 bond pdb=" CB PRO D 696 " pdb=" CG PRO D 696 " ideal model delta sigma weight residual 1.506 1.628 -0.122 3.90e-02 6.57e+02 9.74e+00 ... (remaining 8133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 11386 3.55 - 7.10: 34 7.10 - 10.64: 7 10.64 - 14.19: 1 14.19 - 17.74: 2 Bond angle restraints: 11430 Sorted by residual: angle pdb=" N PRO D 696 " pdb=" CD PRO D 696 " pdb=" CG PRO D 696 " ideal model delta sigma weight residual 103.80 87.95 15.85 1.20e+00 6.94e-01 1.74e+02 angle pdb=" CA PRO D 696 " pdb=" N PRO D 696 " pdb=" CD PRO D 696 " ideal model delta sigma weight residual 111.50 93.76 17.74 1.40e+00 5.10e-01 1.61e+02 angle pdb=" C1' G E 18 " pdb=" N9 G E 18 " pdb=" C4 G E 18 " ideal model delta sigma weight residual 126.50 135.41 -8.91 1.30e+00 5.92e-01 4.70e+01 angle pdb=" C1' G E 18 " pdb=" N9 G E 18 " pdb=" C8 G E 18 " ideal model delta sigma weight residual 127.00 118.40 8.60 1.30e+00 5.92e-01 4.37e+01 angle pdb=" N9 G E 18 " pdb=" C4 G E 18 " pdb=" N3 G E 18 " ideal model delta sigma weight residual 126.00 129.49 -3.49 6.00e-01 2.78e+00 3.39e+01 ... (remaining 11425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.86: 4717 33.86 - 67.72: 313 67.72 - 101.58: 41 101.58 - 135.44: 0 135.44 - 169.30: 2 Dihedral angle restraints: 5073 sinusoidal: 2960 harmonic: 2113 Sorted by residual: dihedral pdb=" CA ARG B 744 " pdb=" C ARG B 744 " pdb=" N GLU B 745 " pdb=" CA GLU B 745 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" C4' C F 49 " pdb=" C3' C F 49 " pdb=" O3' C F 49 " pdb=" P G F 50 " ideal model delta sinusoidal sigma weight residual 220.00 50.70 169.30 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' C E 49 " pdb=" C3' C E 49 " pdb=" O3' C E 49 " pdb=" P G E 50 " ideal model delta sinusoidal sigma weight residual 220.00 56.05 163.95 1 3.50e+01 8.16e-04 1.54e+01 ... (remaining 5070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.290: 1378 0.290 - 0.581: 1 0.581 - 0.871: 0 0.871 - 1.161: 0 1.161 - 1.452: 1 Chirality restraints: 1380 Sorted by residual: chirality pdb=" CB VAL D 162 " pdb=" CA VAL D 162 " pdb=" CG1 VAL D 162 " pdb=" CG2 VAL D 162 " both_signs ideal model delta sigma weight residual False -2.63 -1.18 -1.45 2.00e-01 2.50e+01 5.27e+01 chirality pdb=" C3' C E 49 " pdb=" C4' C E 49 " pdb=" O3' C E 49 " pdb=" C2' C E 49 " both_signs ideal model delta sigma weight residual False -2.48 -2.14 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA PRO D 696 " pdb=" N PRO D 696 " pdb=" C PRO D 696 " pdb=" CB PRO D 696 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1377 not shown) Planarity restraints: 1105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 695 " -0.055 5.00e-02 4.00e+02 7.51e-02 9.01e+00 pdb=" N PRO D 696 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 696 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 696 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U E 19 " -0.028 2.00e-02 2.50e+03 1.51e-02 5.15e+00 pdb=" N1 U E 19 " 0.034 2.00e-02 2.50e+03 pdb=" C2 U E 19 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U E 19 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U E 19 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U E 19 " -0.006 2.00e-02 2.50e+03 pdb=" O4 U E 19 " -0.006 2.00e-02 2.50e+03 pdb=" C5 U E 19 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U E 19 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C E 38 " -0.024 2.00e-02 2.50e+03 1.28e-02 3.68e+00 pdb=" N1 C E 38 " 0.028 2.00e-02 2.50e+03 pdb=" C2 C E 38 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C E 38 " 0.001 2.00e-02 2.50e+03 pdb=" N3 C E 38 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C E 38 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C E 38 " -0.009 2.00e-02 2.50e+03 pdb=" C5 C E 38 " 0.005 2.00e-02 2.50e+03 pdb=" C6 C E 38 " 0.000 2.00e-02 2.50e+03 ... (remaining 1102 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 69 2.57 - 3.15: 6671 3.15 - 3.74: 13118 3.74 - 4.32: 17203 4.32 - 4.90: 26741 Nonbonded interactions: 63802 Sorted by model distance: nonbonded pdb=" O2' U E 48 " pdb=" OP1 G E 50 " model vdw 1.988 3.040 nonbonded pdb=" O2' C F 49 " pdb=" OP1 G F 50 " model vdw 2.010 3.040 nonbonded pdb=" O2' U F 19 " pdb=" OP2 A F 20 " model vdw 2.018 3.040 nonbonded pdb=" O2' U E 19 " pdb=" OP2 A E 20 " model vdw 2.068 3.040 nonbonded pdb=" O LYS C 142 " pdb=" OG1 THR C 145 " model vdw 2.114 3.040 ... (remaining 63797 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 703 or (resid 704 and (name N or name CA or na \ me C or name O or name CB )) or resid 705 through 747)) selection = (chain 'B' and (resid 695 through 702 or (resid 703 through 704 and (name N or n \ ame CA or name C or name O or name CB )) or resid 705 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: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.140 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 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 : 0.005 0.332 8138 Z= 0.244 Angle : 0.730 17.738 11430 Z= 0.573 Chirality : 0.058 1.452 1380 Planarity : 0.004 0.075 1105 Dihedral : 20.201 169.297 3701 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 15.11 % Favored : 84.89 % 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: 1.39 (0.33), residues: 704 helix: 1.48 (0.25), residues: 443 sheet: -0.21 (0.95), residues: 31 loop : 0.16 (0.43), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 744 TYR 0.010 0.001 TYR D 6 PHE 0.012 0.001 PHE D 17 TRP 0.004 0.001 TRP D 522 HIS 0.010 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.24 ( 8138) covalent geometry : angle 0.72977 / 0.57 (11430) hydrogen bonds : bond 0.17659 / 11.50 ( 458) hydrogen bonds : angle 6.48774 / 4.81 ( 1214) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 LEU cc_start: 0.8649 (mt) cc_final: 0.8306 (mt) REVERT: A 735 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8279 (tm-30) REVERT: C 106 ASN cc_start: 0.8491 (m-40) cc_final: 0.8167 (m-40) REVERT: C 141 ILE cc_start: 0.7670 (tp) cc_final: 0.7461 (tp) REVERT: D 19 GLU cc_start: 0.7074 (tt0) cc_final: 0.6690 (mt-10) REVERT: D 632 LEU cc_start: 0.8062 (mt) cc_final: 0.7573 (mt) REVERT: D 692 TRP cc_start: 0.6329 (m100) cc_final: 0.6030 (m100) REVERT: D 735 GLU cc_start: 0.8313 (tp30) cc_final: 0.7699 (tt0) REVERT: D 743 MET cc_start: 0.8018 (tpp) cc_final: 0.7608 (ttm) REVERT: D 746 LYS cc_start: 0.6788 (mttt) cc_final: 0.6192 (mttt) REVERT: D 811 GLU cc_start: 0.7974 (pt0) cc_final: 0.7550 (pp20) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.0860 time to fit residues: 14.1415 Evaluate side-chains 102 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.1980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.2516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 647 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.234016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.188635 restraints weight = 9679.162| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 3.11 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8138 Z= 0.148 Angle : 0.622 8.175 11430 Z= 0.337 Chirality : 0.040 0.213 1380 Planarity : 0.004 0.042 1105 Dihedral : 20.145 177.723 2282 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.46 % Allowed : 15.76 % Favored : 81.77 % 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: 1.25 (0.32), residues: 704 helix: 1.43 (0.24), residues: 457 sheet: -0.80 (0.78), residues: 25 loop : -0.11 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 744 TYR 0.033 0.002 TYR D 626 PHE 0.012 0.002 PHE D 17 TRP 0.006 0.001 TRP D 522 HIS 0.006 0.002 HIS C 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 ( 8138) covalent geometry : angle 0.62225 / 0.34 (11430) hydrogen bonds : bond 0.06629 / 4.33 ( 458) hydrogen bonds : angle 4.99390 / 3.69 ( 1214) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 742 MET cc_start: 0.6060 (tmm) cc_final: 0.5792 (tmm) REVERT: D 48 GLN cc_start: 0.8466 (tm-30) cc_final: 0.7981 (tm-30) REVERT: D 743 MET cc_start: 0.7880 (tpp) cc_final: 0.7491 (ttm) outliers start: 15 outliers final: 11 residues processed: 119 average time/residue: 0.0830 time to fit residues: 13.5731 Evaluate side-chains 104 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 76 GLN Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 616 HIS Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 815 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 28 optimal weight: 0.0980 chunk 45 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4591 r_free = 0.4591 target = 0.230554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.175038 restraints weight = 9620.444| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 1.61 r_work: 0.3615 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8138 Z= 0.173 Angle : 0.599 7.871 11430 Z= 0.323 Chirality : 0.040 0.258 1380 Planarity : 0.005 0.063 1105 Dihedral : 20.080 178.916 2282 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.61 % Allowed : 17.24 % Favored : 79.15 % 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: 1.03 (0.31), residues: 704 helix: 1.27 (0.24), residues: 459 sheet: -1.11 (0.81), residues: 25 loop : -0.19 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 744 TYR 0.013 0.002 TYR A 698 PHE 0.015 0.002 PHE D 17 TRP 0.016 0.003 TRP D 692 HIS 0.004 0.001 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 8138) covalent geometry : angle 0.59876 / 0.32 (11430) hydrogen bonds : bond 0.06401 / 4.21 ( 458) hydrogen bonds : angle 4.68397 / 3.46 ( 1214) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 143 GLU cc_start: 0.6686 (mp0) cc_final: 0.6471 (mp0) REVERT: C 163 MET cc_start: 0.7672 (ttp) cc_final: 0.7312 (tpt) REVERT: D 48 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8271 (tm-30) REVERT: D 702 MET cc_start: 0.4692 (mtm) cc_final: 0.4174 (mpp) REVERT: D 741 ILE cc_start: 0.8071 (mt) cc_final: 0.7697 (tp) REVERT: D 743 MET cc_start: 0.7810 (tpp) cc_final: 0.7387 (ttm) outliers start: 22 outliers final: 18 residues processed: 114 average time/residue: 0.0745 time to fit residues: 11.7192 Evaluate side-chains 112 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 76 GLN Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 616 HIS Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 746 LYS Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 815 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 35 optimal weight: 0.2980 chunk 51 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 0.0170 chunk 54 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 40 optimal weight: 0.0060 chunk 61 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.3834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 721 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.233079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.178275 restraints weight = 9751.647| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 1.50 r_work: 0.3666 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8138 Z= 0.132 Angle : 0.540 6.431 11430 Z= 0.295 Chirality : 0.037 0.228 1380 Planarity : 0.004 0.048 1105 Dihedral : 20.044 179.644 2282 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.12 % Allowed : 20.36 % Favored : 76.52 % 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: 1.10 (0.32), residues: 704 helix: 1.37 (0.24), residues: 459 sheet: -1.20 (0.79), residues: 25 loop : -0.27 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 757 TYR 0.013 0.001 TYR D 626 PHE 0.015 0.001 PHE D 17 TRP 0.012 0.002 TRP D 692 HIS 0.004 0.001 HIS C 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 8138) covalent geometry : angle 0.53962 / 0.29 (11430) hydrogen bonds : bond 0.05827 / 3.81 ( 458) hydrogen bonds : angle 4.52689 / 3.31 ( 1214) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 742 MET cc_start: 0.5980 (tmm) cc_final: 0.5715 (tmm) REVERT: C 101 LYS cc_start: 0.6271 (tttp) cc_final: 0.5725 (tttm) REVERT: C 163 MET cc_start: 0.7661 (ttp) cc_final: 0.7398 (tpt) REVERT: D 48 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8251 (tm-30) REVERT: D 538 GLN cc_start: 0.7102 (tp40) cc_final: 0.6715 (tp40) REVERT: D 741 ILE cc_start: 0.7961 (mt) cc_final: 0.7639 (tp) REVERT: D 743 MET cc_start: 0.7671 (tpp) cc_final: 0.7231 (ttm) outliers start: 19 outliers final: 16 residues processed: 108 average time/residue: 0.0723 time to fit residues: 10.7819 Evaluate side-chains 107 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 701 GLN Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 744 ARG Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 76 GLN Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 616 HIS Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 764 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 28 optimal weight: 0.0870 chunk 12 optimal weight: 0.8980 chunk 21 optimal weight: 0.0040 chunk 15 optimal weight: 0.5980 chunk 57 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 overall best weight: 0.4370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 135 HIS ** 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 = 0.4615 r_free = 0.4615 target = 0.232962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.194503 restraints weight = 9591.322| |-----------------------------------------------------------------------------| r_work (start): 0.4252 rms_B_bonded: 3.03 r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8138 Z= 0.134 Angle : 0.533 6.690 11430 Z= 0.291 Chirality : 0.037 0.223 1380 Planarity : 0.004 0.050 1105 Dihedral : 19.985 178.433 2282 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.85 % Favored : 98.01 % Rotamer: Outliers : 4.43 % Allowed : 20.03 % Favored : 75.53 % 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: 1.09 (0.31), residues: 704 helix: 1.35 (0.24), residues: 461 sheet: -1.22 (0.78), residues: 25 loop : -0.23 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 757 TYR 0.011 0.001 TYR D 64 PHE 0.014 0.001 PHE D 17 TRP 0.008 0.002 TRP D 692 HIS 0.003 0.001 HIS C 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 8138) covalent geometry : angle 0.53278 / 0.29 (11430) hydrogen bonds : bond 0.05657 / 3.70 ( 458) hydrogen bonds : angle 4.43380 / 3.25 ( 1214) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 735 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8238 (tm-30) REVERT: C 80 TYR cc_start: 0.8284 (m-80) cc_final: 0.7598 (m-80) REVERT: D 48 GLN cc_start: 0.8497 (tm-30) cc_final: 0.7955 (tm-30) REVERT: D 596 MET cc_start: 0.1955 (ptp) cc_final: 0.1522 (ptp) REVERT: D 692 TRP cc_start: 0.5057 (m100) cc_final: 0.4554 (m100) REVERT: D 743 MET cc_start: 0.7726 (tpp) cc_final: 0.7384 (ttm) outliers start: 27 outliers final: 23 residues processed: 112 average time/residue: 0.0880 time to fit residues: 13.5698 Evaluate side-chains 116 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 701 GLN Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 744 ARG Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 76 GLN Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 616 HIS Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 749 GLU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 815 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 3 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 11 optimal weight: 0.2980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 135 HIS ** 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 = 0.4680 r_free = 0.4680 target = 0.238616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.195460 restraints weight = 9715.091| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 3.07 r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8138 Z= 0.128 Angle : 0.524 6.395 11430 Z= 0.285 Chirality : 0.036 0.245 1380 Planarity : 0.004 0.038 1105 Dihedral : 19.956 177.571 2282 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.70 % Favored : 98.15 % Rotamer: Outliers : 4.76 % Allowed : 18.72 % Favored : 76.52 % 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: 1.12 (0.31), residues: 704 helix: 1.37 (0.24), residues: 461 sheet: -1.18 (0.81), residues: 25 loop : -0.24 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 744 TYR 0.011 0.001 TYR A 698 PHE 0.014 0.001 PHE D 17 TRP 0.008 0.002 TRP D 692 HIS 0.008 0.001 HIS D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 8138) covalent geometry : angle 0.52357 / 0.28 (11430) hydrogen bonds : bond 0.05460 / 3.57 ( 458) hydrogen bonds : angle 4.35275 / 3.18 ( 1214) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 735 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8169 (tm-30) REVERT: A 740 MET cc_start: 0.6246 (ttp) cc_final: 0.5610 (ttp) REVERT: C 80 TYR cc_start: 0.8343 (m-80) cc_final: 0.7829 (m-80) REVERT: D 48 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8028 (tm-30) REVERT: D 596 MET cc_start: 0.1790 (ptp) cc_final: 0.1384 (ptp) REVERT: D 692 TRP cc_start: 0.5249 (m100) cc_final: 0.4764 (m100) REVERT: D 743 MET cc_start: 0.7815 (tpp) cc_final: 0.7356 (ttm) outliers start: 29 outliers final: 24 residues processed: 116 average time/residue: 0.0671 time to fit residues: 10.9270 Evaluate side-chains 114 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 701 GLN Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 744 ARG Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 76 GLN Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 616 HIS Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 749 GLU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 815 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 71 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 135 HIS ** 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 = 0.4671 r_free = 0.4671 target = 0.237482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.193705 restraints weight = 9783.395| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 3.05 r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8138 Z= 0.151 Angle : 0.540 7.658 11430 Z= 0.294 Chirality : 0.037 0.249 1380 Planarity : 0.004 0.039 1105 Dihedral : 19.939 176.204 2282 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.85 % Favored : 98.01 % Rotamer: Outliers : 3.94 % Allowed : 20.20 % Favored : 75.86 % 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: 0.99 (0.31), residues: 704 helix: 1.27 (0.24), residues: 463 sheet: -1.34 (0.80), residues: 25 loop : -0.28 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 744 TYR 0.013 0.001 TYR A 698 PHE 0.015 0.002 PHE D 17 TRP 0.008 0.002 TRP D 692 HIS 0.004 0.001 HIS D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 8138) covalent geometry : angle 0.54005 / 0.29 (11430) hydrogen bonds : bond 0.05614 / 3.68 ( 458) hydrogen bonds : angle 4.36134 / 3.18 ( 1214) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 735 GLN cc_start: 0.8401 (tm-30) cc_final: 0.8170 (tm-30) REVERT: C 80 TYR cc_start: 0.8343 (m-80) cc_final: 0.7835 (m-80) REVERT: D 48 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8101 (tm-30) REVERT: D 596 MET cc_start: 0.2017 (ptp) cc_final: 0.1807 (ptp) REVERT: D 692 TRP cc_start: 0.5232 (m100) cc_final: 0.4734 (m100) outliers start: 24 outliers final: 23 residues processed: 107 average time/residue: 0.0668 time to fit residues: 9.8658 Evaluate side-chains 108 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 701 GLN Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 744 ARG Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 76 GLN Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 616 HIS Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 749 GLU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 815 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 69 optimal weight: 0.0970 chunk 6 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 135 HIS ** 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 = 0.4673 r_free = 0.4673 target = 0.238374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.186516 restraints weight = 9858.687| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 1.58 r_work: 0.3737 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8138 Z= 0.161 Angle : 0.567 9.018 11430 Z= 0.303 Chirality : 0.038 0.248 1380 Planarity : 0.004 0.041 1105 Dihedral : 19.924 175.957 2282 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.13 % Favored : 97.73 % Rotamer: Outliers : 4.11 % Allowed : 20.53 % Favored : 75.37 % 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: 0.84 (0.31), residues: 704 helix: 1.15 (0.24), residues: 463 sheet: -1.45 (0.81), residues: 25 loop : -0.33 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 744 TYR 0.025 0.002 TYR D 549 PHE 0.015 0.002 PHE D 17 TRP 0.008 0.001 TRP D 692 HIS 0.003 0.001 HIS D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 8138) covalent geometry : angle 0.56676 / 0.30 (11430) hydrogen bonds : bond 0.05667 / 3.69 ( 458) hydrogen bonds : angle 4.34269 / 3.19 ( 1214) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 735 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8304 (tm-30) REVERT: A 740 MET cc_start: 0.6639 (ttp) cc_final: 0.5964 (ttp) REVERT: C 128 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7548 (mm-40) REVERT: C 143 GLU cc_start: 0.6659 (mp0) cc_final: 0.6086 (mp0) REVERT: C 163 MET cc_start: 0.7241 (tpp) cc_final: 0.6960 (ttp) REVERT: D 48 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8276 (tm-30) REVERT: D 692 TRP cc_start: 0.6033 (m100) cc_final: 0.5344 (m100) outliers start: 25 outliers final: 22 residues processed: 105 average time/residue: 0.0741 time to fit residues: 10.5890 Evaluate side-chains 105 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 701 GLN Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 744 ARG Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 76 GLN Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 616 HIS Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 815 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 7 optimal weight: 0.0870 chunk 1 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 47 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 135 HIS ** 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 = 0.4676 r_free = 0.4676 target = 0.238224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.194981 restraints weight = 9782.874| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 2.99 r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8138 Z= 0.139 Angle : 0.559 9.312 11430 Z= 0.302 Chirality : 0.037 0.232 1380 Planarity : 0.004 0.040 1105 Dihedral : 19.916 175.948 2282 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.85 % Favored : 98.01 % Rotamer: Outliers : 4.27 % Allowed : 20.36 % Favored : 75.37 % 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: 0.85 (0.31), residues: 704 helix: 1.10 (0.24), residues: 465 sheet: -1.37 (0.82), residues: 25 loop : -0.21 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 744 TYR 0.012 0.001 TYR A 698 PHE 0.015 0.001 PHE D 17 TRP 0.007 0.001 TRP D 692 HIS 0.004 0.001 HIS D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 8138) covalent geometry : angle 0.55905 / 0.30 (11430) hydrogen bonds : bond 0.05479 / 3.54 ( 458) hydrogen bonds : angle 4.35950 / 3.18 ( 1214) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 735 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8178 (tm-30) REVERT: A 740 MET cc_start: 0.6218 (ttp) cc_final: 0.5518 (ttp) REVERT: C 80 TYR cc_start: 0.8339 (m-80) cc_final: 0.7824 (m-80) REVERT: C 123 LEU cc_start: 0.7834 (mt) cc_final: 0.7634 (mt) REVERT: C 128 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.6997 (mm-40) REVERT: D 4 MET cc_start: 0.4854 (ppp) cc_final: 0.4579 (ppp) REVERT: D 48 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8090 (tm-30) REVERT: D 692 TRP cc_start: 0.5157 (m100) cc_final: 0.4693 (m100) REVERT: D 743 MET cc_start: 0.8046 (tpp) cc_final: 0.7616 (ttm) REVERT: D 765 ASP cc_start: 0.6236 (p0) cc_final: 0.5831 (p0) outliers start: 26 outliers final: 23 residues processed: 107 average time/residue: 0.0787 time to fit residues: 11.6358 Evaluate side-chains 107 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 744 ARG Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 76 GLN Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 580 THR Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 616 HIS Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 749 GLU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 815 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 75 optimal weight: 8.9990 chunk 7 optimal weight: 0.1980 chunk 72 optimal weight: 4.9990 chunk 10 optimal weight: 0.1980 chunk 11 optimal weight: 0.1980 chunk 48 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 79 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 135 HIS ** 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 = 0.4678 r_free = 0.4678 target = 0.238556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.194827 restraints weight = 9726.389| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 3.02 r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8138 Z= 0.130 Angle : 0.570 12.938 11430 Z= 0.303 Chirality : 0.037 0.224 1380 Planarity : 0.004 0.059 1105 Dihedral : 19.878 175.449 2282 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.85 % Favored : 98.01 % Rotamer: Outliers : 3.78 % Allowed : 21.02 % Favored : 75.21 % 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: 0.86 (0.32), residues: 704 helix: 1.12 (0.24), residues: 464 sheet: -1.25 (0.84), residues: 25 loop : -0.21 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 757 TYR 0.039 0.001 TYR D 549 PHE 0.014 0.001 PHE D 17 TRP 0.007 0.001 TRP D 692 HIS 0.003 0.001 HIS D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 8138) covalent geometry : angle 0.57019 / 0.30 (11430) hydrogen bonds : bond 0.05309 / 3.42 ( 458) hydrogen bonds : angle 4.37955 / 3.17 ( 1214) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 735 GLN cc_start: 0.8384 (tm-30) cc_final: 0.8168 (tm-30) REVERT: A 740 MET cc_start: 0.6237 (ttp) cc_final: 0.5556 (ttp) REVERT: C 123 LEU cc_start: 0.7829 (mt) cc_final: 0.7618 (mt) REVERT: D 48 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8099 (tm-30) REVERT: D 692 TRP cc_start: 0.5210 (m100) cc_final: 0.4752 (m100) REVERT: D 743 MET cc_start: 0.8050 (tpp) cc_final: 0.7626 (ttm) REVERT: D 765 ASP cc_start: 0.6310 (p0) cc_final: 0.5887 (p0) outliers start: 23 outliers final: 22 residues processed: 102 average time/residue: 0.0885 time to fit residues: 12.2230 Evaluate side-chains 104 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 744 ARG Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 76 GLN Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 580 THR Chi-restraints excluded: chain D residue 616 HIS Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 749 GLU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 815 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 47 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 11 optimal weight: 0.2980 chunk 74 optimal weight: 7.9990 chunk 39 optimal weight: 0.0020 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 57 optimal weight: 0.0040 chunk 77 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 135 HIS ** 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 = 0.4679 r_free = 0.4679 target = 0.238816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.200663 restraints weight = 9756.473| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 2.94 r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8138 Z= 0.133 Angle : 0.579 9.772 11430 Z= 0.309 Chirality : 0.037 0.223 1380 Planarity : 0.004 0.036 1105 Dihedral : 19.853 174.840 2282 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.41 % Favored : 97.44 % Rotamer: Outliers : 3.61 % Allowed : 21.51 % Favored : 74.88 % 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: 0.93 (0.32), residues: 704 helix: 1.16 (0.24), residues: 464 sheet: -1.17 (0.88), residues: 25 loop : -0.17 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 757 TYR 0.045 0.002 TYR D 549 PHE 0.014 0.001 PHE D 17 TRP 0.007 0.001 TRP D 692 HIS 0.003 0.001 HIS D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 8138) covalent geometry : angle 0.57886 / 0.31 (11430) hydrogen bonds : bond 0.05263 / 3.39 ( 458) hydrogen bonds : angle 4.40104 / 3.20 ( 1214) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1458.53 seconds wall clock time: 25 minutes 49.55 seconds (1549.55 seconds total)