Starting phenix.real_space_refine on Tue Aug 4 23:50:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rw3_54297/08_2026/9rw3_54297.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rw3_54297/08_2026/9rw3_54297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rw3_54297/08_2026/9rw3_54297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rw3_54297/08_2026/9rw3_54297.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rw3_54297/08_2026/9rw3_54297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rw3_54297/08_2026/9rw3_54297.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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 84 5.49 5 S 30 5.16 5 C 4407 2.51 5 N 1303 2.21 5 O 1671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s 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: 7495 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 389 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 389 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 3654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3654 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 443} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1255 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 152} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 904 Classifications: {'RNA': 43} Modifications used: {'5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 19, 'rna3p_pyr': 22} Link IDs: {'rna2p': 2, 'rna3p': 40} Chain breaks: 1 Chain: "F" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 904 Classifications: {'RNA': 43} Modifications used: {'5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 19, 'rna3p_pyr': 22} Link IDs: {'rna2p': 2, 'rna3p': 40} Chain breaks: 1 Time building chain proxies: 1.73, per 1000 atoms: 0.23 Number of scatterers: 7495 At special positions: 0 Unit cell: (82.68, 96.46, 156.88, 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 30 16.00 P 84 15.00 O 1671 8.00 N 1303 7.00 C 4407 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: 0.66 Conformation dependent library (CDL) restraints added in 403.0 milliseconds 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1366 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 4 sheets defined 72.2% alpha, 4.9% beta 34 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 695 through 747 removed outlier: 3.927A pdb=" N VAL A 699 " --> pdb=" O CYS A 695 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 747 removed outlier: 3.613A pdb=" N ARG B 747 " --> pdb=" O ASP B 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 25 removed outlier: 4.010A 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 63 Processing helix chain 'D' and resid 95 through 112 removed outlier: 3.769A pdb=" N TYR D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY D 112 " --> pdb=" O MET D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 125 removed outlier: 3.699A 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 137 Processing helix chain 'D' and resid 140 through 152 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: 4.019A 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 630 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 Processing helix chain 'D' and resid 676 through 688 removed outlier: 4.033A pdb=" N GLN D 680 " --> pdb=" O PRO D 676 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE D 684 " --> pdb=" O GLN D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 693 Processing helix chain 'D' and resid 698 through 714 Processing helix chain 'D' and resid 714 through 723 Processing helix chain 'D' and resid 726 through 743 Processing helix chain 'D' and resid 746 through 773 removed outlier: 3.500A 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 3 through 25 Processing helix chain 'C' and resid 30 through 36 Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 53 through 63 Processing helix chain 'C' and resid 95 through 112 removed outlier: 3.811A pdb=" N GLU C 99 " --> pdb=" O ASP C 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY C 112 " --> pdb=" O MET C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 125 removed outlier: 3.719A pdb=" N HIS C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 129 Processing helix chain 'C' and resid 130 through 137 Processing helix chain 'C' and resid 140 through 152 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 531 through 533 removed outlier: 5.439A pdb=" N ILE D 573 " --> pdb=" O ILE D 565 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE D 565 " --> pdb=" O ILE D 573 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 556 through 559 removed outlier: 6.677A pdb=" N ILE D 556 " --> pdb=" O ILE D 612 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL D 614 " --> pdb=" O ILE D 556 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL D 558 " --> pdb=" O VAL D 614 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 28 through 29 376 hydrogen bonds defined for protein. 1089 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 0.90 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: 1082 1.31 - 1.43: 2448 1.43 - 1.56: 4036 1.56 - 1.69: 166 1.69 - 1.81: 51 Bond restraints: 7783 Sorted by residual: bond pdb=" CA MET C 46 " pdb=" C MET C 46 " ideal model delta sigma weight residual 1.524 1.453 0.070 1.29e-02 6.01e+03 2.97e+01 bond pdb=" N ILE D 578 " pdb=" CA ILE D 578 " ideal model delta sigma weight residual 1.459 1.398 0.062 1.29e-02 6.01e+03 2.28e+01 bond pdb=" C ILE D 578 " pdb=" O ILE D 578 " ideal model delta sigma weight residual 1.234 1.180 0.054 1.16e-02 7.43e+03 2.19e+01 bond pdb=" C MET C 46 " pdb=" O MET C 46 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.19e-02 7.06e+03 2.18e+01 bond pdb=" N1 C F 29 " pdb=" C6 C F 29 " ideal model delta sigma weight residual 1.367 1.389 -0.022 6.00e-03 2.78e+04 1.34e+01 ... (remaining 7778 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 10021 1.35 - 2.69: 722 2.69 - 4.04: 123 4.04 - 5.38: 14 5.38 - 6.73: 3 Bond angle restraints: 10883 Sorted by residual: angle pdb=" O5' C F 38 " pdb=" C5' C F 38 " pdb=" C4' C F 38 " ideal model delta sigma weight residual 109.40 114.97 -5.57 8.00e-01 1.56e+00 4.84e+01 angle pdb=" N6 A F 8 " pdb=" C6 A F 8 " pdb=" N1 A F 8 " ideal model delta sigma weight residual 118.60 114.74 3.86 6.00e-01 2.78e+00 4.14e+01 angle pdb=" N6 A F 30 " pdb=" C6 A F 30 " pdb=" N1 A F 30 " ideal model delta sigma weight residual 118.60 114.74 3.86 6.00e-01 2.78e+00 4.14e+01 angle pdb=" N6 A F 13 " pdb=" C6 A F 13 " pdb=" N1 A F 13 " ideal model delta sigma weight residual 118.60 115.32 3.28 6.00e-01 2.78e+00 2.99e+01 angle pdb=" N6 A F 10 " pdb=" C6 A F 10 " pdb=" N1 A F 10 " ideal model delta sigma weight residual 118.60 115.35 3.25 6.00e-01 2.78e+00 2.94e+01 ... (remaining 10878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.70: 4284 23.70 - 47.40: 428 47.40 - 71.10: 128 71.10 - 94.80: 22 94.80 - 118.50: 5 Dihedral angle restraints: 4867 sinusoidal: 2764 harmonic: 2103 Sorted by residual: dihedral pdb=" CA ALA C 79 " pdb=" C ALA C 79 " pdb=" N TYR C 80 " pdb=" CA TYR C 80 " ideal model delta harmonic sigma weight residual 180.00 -155.90 -24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" C3' U F 39 " pdb=" C4' U F 39 " pdb=" O4' U F 39 " pdb=" C1' U F 39 " ideal model delta sinusoidal sigma weight residual 20.00 -2.57 22.57 1 8.00e+00 1.56e-02 1.15e+01 dihedral pdb=" CA ASN C 78 " pdb=" C ASN C 78 " pdb=" N ALA C 79 " pdb=" CA ALA C 79 " ideal model delta harmonic sigma weight residual 180.00 163.16 16.84 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 4864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 927 0.041 - 0.082: 223 0.082 - 0.123: 120 0.123 - 0.164: 29 0.164 - 0.205: 2 Chirality restraints: 1301 Sorted by residual: chirality pdb=" CB ILE D 578 " pdb=" CA ILE D 578 " pdb=" CG1 ILE D 578 " pdb=" CG2 ILE D 578 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C3' G F 26 " pdb=" C4' G F 26 " pdb=" O3' G F 26 " pdb=" C2' G F 26 " both_signs ideal model delta sigma weight residual False -2.48 -2.66 0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" C2' C F 19 " pdb=" C3' C F 19 " pdb=" O2' C F 19 " pdb=" C1' C F 19 " both_signs ideal model delta sigma weight residual False -2.62 -2.78 0.16 2.00e-01 2.50e+01 6.32e-01 ... (remaining 1298 not shown) Planarity restraints: 1088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C F 16 " 0.072 2.00e-02 2.50e+03 3.61e-02 2.93e+01 pdb=" N1 C F 16 " -0.023 2.00e-02 2.50e+03 pdb=" C2 C F 16 " -0.012 2.00e-02 2.50e+03 pdb=" O2 C F 16 " -0.024 2.00e-02 2.50e+03 pdb=" N3 C F 16 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C F 16 " -0.019 2.00e-02 2.50e+03 pdb=" N4 C F 16 " 0.060 2.00e-02 2.50e+03 pdb=" C5 C F 16 " -0.025 2.00e-02 2.50e+03 pdb=" C6 C F 16 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G F 34 " -0.073 2.00e-02 2.50e+03 2.94e-02 2.59e+01 pdb=" N9 G F 34 " 0.030 2.00e-02 2.50e+03 pdb=" C8 G F 34 " 0.033 2.00e-02 2.50e+03 pdb=" N7 G F 34 " 0.021 2.00e-02 2.50e+03 pdb=" C5 G F 34 " 0.005 2.00e-02 2.50e+03 pdb=" C6 G F 34 " -0.015 2.00e-02 2.50e+03 pdb=" O6 G F 34 " -0.032 2.00e-02 2.50e+03 pdb=" N1 G F 34 " -0.015 2.00e-02 2.50e+03 pdb=" C2 G F 34 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G F 34 " 0.029 2.00e-02 2.50e+03 pdb=" N3 G F 34 " 0.011 2.00e-02 2.50e+03 pdb=" C4 G F 34 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U F 6 " -0.064 2.00e-02 2.50e+03 2.99e-02 2.01e+01 pdb=" N1 U F 6 " 0.026 2.00e-02 2.50e+03 pdb=" C2 U F 6 " 0.007 2.00e-02 2.50e+03 pdb=" O2 U F 6 " 0.029 2.00e-02 2.50e+03 pdb=" N3 U F 6 " -0.008 2.00e-02 2.50e+03 pdb=" C4 U F 6 " -0.009 2.00e-02 2.50e+03 pdb=" O4 U F 6 " -0.029 2.00e-02 2.50e+03 pdb=" C5 U F 6 " 0.016 2.00e-02 2.50e+03 pdb=" C6 U F 6 " 0.034 2.00e-02 2.50e+03 ... (remaining 1085 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 193 2.67 - 3.22: 7439 3.22 - 3.78: 12846 3.78 - 4.34: 16537 4.34 - 4.90: 25832 Nonbonded interactions: 62847 Sorted by model distance: nonbonded pdb=" OD2 ASP D 589 " pdb=" OG SER D 592 " model vdw 2.107 3.040 nonbonded pdb=" O MET D 149 " pdb=" OG1 THR D 152 " model vdw 2.125 3.040 nonbonded pdb=" OD1 ASN D 620 " pdb=" O2' U E 39 " model vdw 2.141 3.040 nonbonded pdb=" OG1 THR C 43 " pdb=" OE1 GLU C 45 " model vdw 2.150 3.040 nonbonded pdb=" OG1 THR D 793 " pdb=" OD1 ASP D 795 " model vdw 2.211 3.040 ... (remaining 62842 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' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.050 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 0.070 7783 Z= 0.351 Angle : 0.742 6.729 10883 Z= 0.687 Chirality : 0.047 0.205 1301 Planarity : 0.005 0.056 1088 Dihedral : 19.449 118.500 3501 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.17 % Allowed : 17.53 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.12 (0.33), residues: 703 helix: 2.30 (0.24), residues: 461 sheet: -1.86 (1.04), residues: 27 loop : -0.10 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 785 TYR 0.014 0.001 TYR C 80 PHE 0.010 0.001 PHE D 147 TRP 0.002 0.001 TRP D 692 HIS 0.005 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.35 ( 7783) covalent geometry : angle 0.74210 / 0.69 (10883) hydrogen bonds : bond 0.10425 / 6.98 ( 458) hydrogen bonds : angle 5.17395 / 4.08 ( 1245) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 113 average time/residue: 0.1046 time to fit residues: 15.4270 Evaluate side-chains 104 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 578 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 708 GLN D 151 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.151122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.112040 restraints weight = 13137.312| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.38 r_work: 0.3286 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7783 Z= 0.218 Angle : 0.585 7.850 10883 Z= 0.323 Chirality : 0.040 0.194 1301 Planarity : 0.004 0.057 1088 Dihedral : 18.744 104.616 2094 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.01 % Allowed : 16.53 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.95 (0.32), residues: 703 helix: 2.10 (0.24), residues: 473 sheet: -1.96 (0.96), residues: 27 loop : -0.10 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 785 TYR 0.015 0.002 TYR C 80 PHE 0.017 0.002 PHE D 147 TRP 0.003 0.001 TRP D 692 HIS 0.007 0.002 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 ( 7783) covalent geometry : angle 0.58548 / 0.32 (10883) hydrogen bonds : bond 0.05996 / 4.26 ( 458) hydrogen bonds : angle 4.63231 / 3.54 ( 1245) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 735 GLN cc_start: 0.7704 (mp10) cc_final: 0.7239 (mp10) REVERT: D 538 GLN cc_start: 0.8034 (pm20) cc_final: 0.7811 (pm20) REVERT: D 680 GLN cc_start: 0.8297 (tm-30) cc_final: 0.8094 (tm-30) REVERT: C 80 TYR cc_start: 0.9088 (OUTLIER) cc_final: 0.8391 (m-80) outliers start: 18 outliers final: 11 residues processed: 124 average time/residue: 0.0940 time to fit residues: 15.3703 Evaluate side-chains 118 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 562 CYS Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 137 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 28 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 47 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 18 optimal weight: 0.0010 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 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 = 0.4220 r_free = 0.4220 target = 0.153922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.113437 restraints weight = 12944.008| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.30 r_work: 0.3337 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 : 0.002 0.026 7783 Z= 0.123 Angle : 0.503 7.424 10883 Z= 0.277 Chirality : 0.035 0.175 1301 Planarity : 0.004 0.059 1088 Dihedral : 18.725 105.535 2094 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.84 % Allowed : 16.36 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.10 (0.32), residues: 703 helix: 2.27 (0.24), residues: 470 sheet: -2.16 (0.93), residues: 27 loop : -0.13 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 736 TYR 0.011 0.001 TYR D 161 PHE 0.013 0.002 PHE C 155 TRP 0.003 0.001 TRP D 522 HIS 0.004 0.001 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 7783) covalent geometry : angle 0.50291 / 0.28 (10883) hydrogen bonds : bond 0.05113 / 3.66 ( 458) hydrogen bonds : angle 4.33990 / 3.30 ( 1245) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 538 GLN cc_start: 0.8157 (pm20) cc_final: 0.7898 (pm20) REVERT: D 596 MET cc_start: 0.6386 (ptm) cc_final: 0.6079 (ptp) REVERT: D 634 ARG cc_start: 0.5656 (tpm170) cc_final: 0.5364 (tpm170) REVERT: D 674 CYS cc_start: 0.6551 (t) cc_final: 0.5661 (p) REVERT: D 680 GLN cc_start: 0.8252 (tm-30) cc_final: 0.8025 (tm-30) REVERT: C 80 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.8501 (m-80) outliers start: 17 outliers final: 11 residues processed: 120 average time/residue: 0.0942 time to fit residues: 14.9241 Evaluate side-chains 119 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 549 TYR Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 157 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 14 optimal weight: 0.3980 chunk 48 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 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 = 0.4223 r_free = 0.4223 target = 0.154127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.113234 restraints weight = 13112.789| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.36 r_work: 0.3335 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7783 Z= 0.120 Angle : 0.480 6.901 10883 Z= 0.261 Chirality : 0.034 0.173 1301 Planarity : 0.004 0.059 1088 Dihedral : 18.679 106.545 2092 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.34 % Allowed : 17.53 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.22 (0.32), residues: 703 helix: 2.36 (0.24), residues: 470 sheet: -2.06 (0.94), residues: 27 loop : -0.10 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 736 TYR 0.010 0.001 TYR C 80 PHE 0.011 0.002 PHE D 147 TRP 0.002 0.001 TRP D 692 HIS 0.004 0.001 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 7783) covalent geometry : angle 0.47992 / 0.26 (10883) hydrogen bonds : bond 0.04844 / 3.47 ( 458) hydrogen bonds : angle 4.24829 / 3.22 ( 1245) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 538 GLN cc_start: 0.8219 (pm20) cc_final: 0.8007 (mp10) REVERT: D 596 MET cc_start: 0.6356 (ptm) cc_final: 0.5997 (ptp) REVERT: D 634 ARG cc_start: 0.5650 (tpm170) cc_final: 0.5350 (tpm170) REVERT: D 674 CYS cc_start: 0.6422 (t) cc_final: 0.5524 (p) REVERT: D 680 GLN cc_start: 0.8322 (tm-30) cc_final: 0.8081 (tm-30) REVERT: D 718 PHE cc_start: 0.5391 (t80) cc_final: 0.5186 (t80) REVERT: C 24 LYS cc_start: 0.7537 (tttt) cc_final: 0.7292 (tttt) REVERT: C 80 TYR cc_start: 0.8887 (OUTLIER) cc_final: 0.8453 (m-80) REVERT: C 123 LEU cc_start: 0.7733 (tp) cc_final: 0.7504 (mt) outliers start: 20 outliers final: 14 residues processed: 119 average time/residue: 0.0941 time to fit residues: 14.9121 Evaluate side-chains 122 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 549 TYR Chi-restraints excluded: chain D residue 562 CYS Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 780 SER Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 157 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 20.0000 chunk 42 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.152968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.112919 restraints weight = 12940.963| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.25 r_work: 0.3319 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7783 Z= 0.141 Angle : 0.487 6.802 10883 Z= 0.264 Chirality : 0.035 0.167 1301 Planarity : 0.004 0.056 1088 Dihedral : 18.667 107.505 2092 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.84 % Allowed : 17.70 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.09 (0.32), residues: 703 helix: 2.24 (0.24), residues: 473 sheet: -1.92 (0.98), residues: 26 loop : -0.17 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 736 TYR 0.013 0.001 TYR C 80 PHE 0.014 0.002 PHE D 147 TRP 0.002 0.001 TRP D 692 HIS 0.006 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 7783) covalent geometry : angle 0.48738 / 0.26 (10883) hydrogen bonds : bond 0.04780 / 3.42 ( 458) hydrogen bonds : angle 4.22746 / 3.20 ( 1245) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 730 LYS cc_start: 0.8961 (tmtt) cc_final: 0.8514 (tttm) REVERT: D 538 GLN cc_start: 0.8236 (pm20) cc_final: 0.7989 (mp10) REVERT: D 596 MET cc_start: 0.6325 (ptm) cc_final: 0.5971 (ptp) REVERT: D 634 ARG cc_start: 0.5731 (tpm170) cc_final: 0.5433 (tpm170) REVERT: D 674 CYS cc_start: 0.6371 (t) cc_final: 0.5480 (p) REVERT: D 680 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7983 (tm-30) REVERT: C 80 TYR cc_start: 0.8971 (OUTLIER) cc_final: 0.8481 (m-80) outliers start: 23 outliers final: 18 residues processed: 124 average time/residue: 0.1011 time to fit residues: 16.5263 Evaluate side-chains 128 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 549 TYR Chi-restraints excluded: chain D residue 562 CYS Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 780 SER Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 157 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 72 optimal weight: 10.9990 chunk 19 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 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 = 0.4202 r_free = 0.4202 target = 0.152365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.113020 restraints weight = 13178.241| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.36 r_work: 0.3305 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7783 Z= 0.181 Angle : 0.518 7.046 10883 Z= 0.279 Chirality : 0.037 0.187 1301 Planarity : 0.004 0.056 1088 Dihedral : 18.675 108.019 2092 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.01 % Allowed : 18.20 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.32), residues: 703 helix: 2.14 (0.24), residues: 471 sheet: -1.93 (0.96), residues: 26 loop : -0.23 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 736 TYR 0.016 0.002 TYR C 80 PHE 0.015 0.002 PHE D 147 TRP 0.003 0.001 TRP D 692 HIS 0.006 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 ( 7783) covalent geometry : angle 0.51805 / 0.28 (10883) hydrogen bonds : bond 0.04895 / 3.50 ( 458) hydrogen bonds : angle 4.26116 / 3.23 ( 1245) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 596 MET cc_start: 0.6268 (ptm) cc_final: 0.5915 (ptp) REVERT: D 674 CYS cc_start: 0.6374 (t) cc_final: 0.5478 (p) REVERT: C 24 LYS cc_start: 0.7543 (tttt) cc_final: 0.7197 (tttt) REVERT: C 80 TYR cc_start: 0.9106 (OUTLIER) cc_final: 0.8527 (m-80) outliers start: 24 outliers final: 20 residues processed: 119 average time/residue: 0.0949 time to fit residues: 14.7645 Evaluate side-chains 123 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 735 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 549 TYR Chi-restraints excluded: chain D residue 562 CYS Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 780 SER Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 157 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 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 = 0.4179 r_free = 0.4179 target = 0.150423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.108864 restraints weight = 13135.521| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.26 r_work: 0.3268 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 7783 Z= 0.249 Angle : 0.591 8.296 10883 Z= 0.314 Chirality : 0.041 0.330 1301 Planarity : 0.005 0.056 1088 Dihedral : 18.722 108.650 2092 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.34 % Allowed : 18.53 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.60 (0.32), residues: 703 helix: 1.83 (0.24), residues: 472 sheet: -1.78 (1.05), residues: 26 loop : -0.29 (0.44), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 120 TYR 0.017 0.002 TYR C 80 PHE 0.020 0.003 PHE D 588 TRP 0.004 0.001 TRP D 692 HIS 0.008 0.002 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.25 ( 7783) covalent geometry : angle 0.59092 / 0.31 (10883) hydrogen bonds : bond 0.05376 / 3.82 ( 458) hydrogen bonds : angle 4.37139 / 3.31 ( 1245) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 735 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7282 (mp10) REVERT: D 527 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.7018 (pp) REVERT: D 538 GLN cc_start: 0.8465 (mp10) cc_final: 0.8166 (pm20) REVERT: D 596 MET cc_start: 0.6242 (ptm) cc_final: 0.5746 (ptp) REVERT: D 786 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7871 (mp) REVERT: C 24 LYS cc_start: 0.7619 (tttt) cc_final: 0.7385 (tttt) REVERT: C 73 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7748 (t0) REVERT: C 80 TYR cc_start: 0.9178 (OUTLIER) cc_final: 0.8623 (m-80) outliers start: 26 outliers final: 19 residues processed: 120 average time/residue: 0.0733 time to fit residues: 11.8590 Evaluate side-chains 123 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 735 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 562 CYS Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 720 ASN Chi-restraints excluded: chain D residue 780 SER Chi-restraints excluded: chain D residue 786 LEU Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 157 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 24 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 75 optimal weight: 20.0000 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 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 = 0.4215 r_free = 0.4215 target = 0.153414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.112660 restraints weight = 13167.749| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.24 r_work: 0.3336 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7783 Z= 0.124 Angle : 0.520 10.247 10883 Z= 0.277 Chirality : 0.035 0.243 1301 Planarity : 0.004 0.056 1088 Dihedral : 18.733 107.260 2092 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.01 % Allowed : 19.53 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.33), residues: 703 helix: 2.03 (0.24), residues: 473 sheet: -1.86 (1.01), residues: 26 loop : -0.21 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 736 TYR 0.019 0.001 TYR C 103 PHE 0.012 0.002 PHE C 147 TRP 0.004 0.001 TRP D 522 HIS 0.005 0.001 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 7783) covalent geometry : angle 0.51972 / 0.28 (10883) hydrogen bonds : bond 0.04565 / 3.30 ( 458) hydrogen bonds : angle 4.17253 / 3.17 ( 1245) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 527 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6959 (pp) REVERT: D 596 MET cc_start: 0.6183 (ptm) cc_final: 0.5864 (ptp) REVERT: C 80 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.8601 (m-80) outliers start: 24 outliers final: 18 residues processed: 119 average time/residue: 0.0904 time to fit residues: 14.2389 Evaluate side-chains 119 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 735 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 549 TYR Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 720 ASN Chi-restraints excluded: chain D residue 780 SER Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 152 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 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 = 0.4215 r_free = 0.4215 target = 0.153426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.115257 restraints weight = 13074.802| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.37 r_work: 0.3334 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7783 Z= 0.131 Angle : 0.545 13.160 10883 Z= 0.284 Chirality : 0.036 0.262 1301 Planarity : 0.004 0.056 1088 Dihedral : 18.689 107.307 2092 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.34 % Allowed : 19.87 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.33), residues: 703 helix: 2.07 (0.24), residues: 473 sheet: -1.83 (1.03), residues: 26 loop : -0.10 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 120 TYR 0.022 0.001 TYR D 704 PHE 0.022 0.002 PHE D 588 TRP 0.004 0.001 TRP D 522 HIS 0.006 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 7783) covalent geometry : angle 0.54526 / 0.28 (10883) hydrogen bonds : bond 0.04554 / 3.28 ( 458) hydrogen bonds : angle 4.14107 / 3.14 ( 1245) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 730 LYS cc_start: 0.8999 (tmtt) cc_final: 0.8550 (tttm) REVERT: D 527 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6961 (pp) REVERT: D 596 MET cc_start: 0.6169 (ptm) cc_final: 0.5845 (ptp) REVERT: D 674 CYS cc_start: 0.6226 (t) cc_final: 0.5353 (p) REVERT: D 786 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7649 (mp) REVERT: C 80 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.8536 (m-80) outliers start: 20 outliers final: 16 residues processed: 117 average time/residue: 0.0889 time to fit residues: 13.8132 Evaluate side-chains 119 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 735 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 549 TYR Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 720 ASN Chi-restraints excluded: chain D residue 780 SER Chi-restraints excluded: chain D residue 786 LEU Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 152 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 708 GLN ** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.154160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.116061 restraints weight = 13046.453| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.38 r_work: 0.3345 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7783 Z= 0.125 Angle : 0.524 14.420 10883 Z= 0.276 Chirality : 0.035 0.250 1301 Planarity : 0.004 0.053 1088 Dihedral : 18.678 107.302 2092 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.67 % Allowed : 19.20 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.95 (0.33), residues: 703 helix: 2.08 (0.24), residues: 473 sheet: -1.67 (1.05), residues: 26 loop : -0.11 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 120 TYR 0.023 0.001 TYR D 704 PHE 0.013 0.002 PHE C 147 TRP 0.004 0.001 TRP D 522 HIS 0.008 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 7783) covalent geometry : angle 0.52406 / 0.28 (10883) hydrogen bonds : bond 0.04406 / 3.18 ( 458) hydrogen bonds : angle 4.13713 / 3.14 ( 1245) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 730 LYS cc_start: 0.8989 (tmtt) cc_final: 0.8533 (tttm) REVERT: D 527 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6904 (pp) REVERT: D 674 CYS cc_start: 0.6024 (t) cc_final: 0.5224 (p) REVERT: D 786 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7609 (mp) REVERT: C 80 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.8524 (m-80) outliers start: 22 outliers final: 19 residues processed: 119 average time/residue: 0.0909 time to fit residues: 14.2823 Evaluate side-chains 126 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 735 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 549 TYR Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 720 ASN Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 780 SER Chi-restraints excluded: chain D residue 786 LEU Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 152 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 0.5980 chunk 72 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 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 = 0.4216 r_free = 0.4216 target = 0.153529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.115181 restraints weight = 13081.752| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.40 r_work: 0.3328 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7783 Z= 0.143 Angle : 0.545 13.849 10883 Z= 0.286 Chirality : 0.037 0.229 1301 Planarity : 0.004 0.052 1088 Dihedral : 18.664 107.111 2092 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.01 % Allowed : 20.03 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.33), residues: 703 helix: 2.07 (0.24), residues: 473 sheet: -1.93 (1.06), residues: 26 loop : -0.14 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 120 TYR 0.025 0.001 TYR D 704 PHE 0.016 0.002 PHE D 588 TRP 0.003 0.001 TRP D 522 HIS 0.005 0.001 HIS D 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 7783) covalent geometry : angle 0.54465 / 0.29 (10883) hydrogen bonds : bond 0.04506 / 3.25 ( 458) hydrogen bonds : angle 4.17918 / 3.17 ( 1245) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1806.82 seconds wall clock time: 31 minutes 41.71 seconds (1901.71 seconds total)