Starting phenix.real_space_refine on Thu Jul 2 21:10:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d69_30591/07_2026/7d69_30591.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d69_30591/07_2026/7d69_30591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d69_30591/07_2026/7d69_30591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d69_30591/07_2026/7d69_30591.map" model { file = "/net/cci-nas-00/data/ceres_data/7d69_30591/07_2026/7d69_30591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d69_30591/07_2026/7d69_30591.cif" } resolution = 3.57 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= 1.000 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 250 5.49 5 S 13 5.16 5 C 6015 2.51 5 N 2012 2.21 5 O 2567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10857 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 716 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "D" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 743 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 779 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 621 Classifications: {'peptide': 78} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 743 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "C" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 754 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "G" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 754 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "I" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2561 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Chain: "J" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2564 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Time building chain proxies: 1.91, per 1000 atoms: 0.18 Number of scatterers: 10857 At special positions: 0 Unit cell: (84, 121.8, 114.45, 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 13 16.00 P 250 15.00 O 2567 8.00 N 2012 7.00 C 6015 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: 0.94 Conformation dependent library (CDL) restraints added in 174.4 milliseconds 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 6 sheets defined 74.0% alpha, 1.9% beta 121 base pairs and 227 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 51 through 58 removed outlier: 3.897A pdb=" N TYR A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 78 Processing helix chain 'A' and resid 88 through 117 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'B' and resid 21 through 25 Processing helix chain 'B' and resid 26 through 37 Processing helix chain 'B' and resid 45 through 72 removed outlier: 3.698A pdb=" N GLY B 72 " --> pdb=" O TYR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 90 Processing helix chain 'D' and resid 30 through 45 removed outlier: 3.607A pdb=" N ILE D 43 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 84 Processing helix chain 'D' and resid 89 through 101 Processing helix chain 'D' and resid 103 through 122 Processing helix chain 'E' and resid 45 through 58 removed outlier: 4.096A pdb=" N VAL E 49 " --> pdb=" O GLY E 45 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS E 50 " --> pdb=" O MET E 46 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER E 58 " --> pdb=" O LYS E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 79 Processing helix chain 'E' and resid 88 through 117 Processing helix chain 'E' and resid 123 through 133 Processing helix chain 'F' and resid 21 through 25 Processing helix chain 'F' and resid 26 through 38 Processing helix chain 'F' and resid 44 through 72 removed outlier: 4.273A pdb=" N GLN F 48 " --> pdb=" O SER F 44 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY F 72 " --> pdb=" O TYR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 88 Processing helix chain 'H' and resid 30 through 43 Processing helix chain 'H' and resid 54 through 84 Processing helix chain 'H' and resid 89 through 101 Processing helix chain 'H' and resid 103 through 122 Processing helix chain 'C' and resid 13 through 18 Processing helix chain 'C' and resid 23 through 34 Processing helix chain 'C' and resid 42 through 68 removed outlier: 4.162A pdb=" N VAL C 46 " --> pdb=" O SER C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 removed outlier: 3.604A pdb=" N ASP C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'G' and resid 13 through 18 Processing helix chain 'G' and resid 23 through 34 Processing helix chain 'G' and resid 43 through 68 removed outlier: 3.618A pdb=" N TYR G 47 " --> pdb=" O ASP G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 87 removed outlier: 4.103A pdb=" N ASP G 87 " --> pdb=" O ALA G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 removed outlier: 7.028A pdb=" N ARG A 86 " --> pdb=" O VAL B 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA3, first strand: chain 'B' and resid 93 through 94 removed outlier: 3.681A pdb=" N TYR B 94 " --> pdb=" O THR G 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 86 through 87 removed outlier: 7.127A pdb=" N ARG E 86 " --> pdb=" O VAL F 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 121 through 122 Processing sheet with id=AA6, first strand: chain 'F' and resid 92 through 94 removed outlier: 6.189A pdb=" N THR F 92 " --> pdb=" O THR C 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 392 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 315 hydrogen bonds 630 hydrogen bond angles 0 basepair planarities 121 basepair parallelities 227 stacking parallelities Total time for adding SS restraints: 1.43 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1840 1.33 - 1.45: 3827 1.45 - 1.57: 5355 1.57 - 1.68: 498 1.68 - 1.80: 22 Bond restraints: 11542 Sorted by residual: bond pdb=" C3' DG J 87 " pdb=" O3' DG J 87 " ideal model delta sigma weight residual 1.435 1.379 0.056 1.30e-02 5.92e+03 1.88e+01 bond pdb=" C3' DA I 22 " pdb=" O3' DA I 22 " ideal model delta sigma weight residual 1.435 1.382 0.053 1.30e-02 5.92e+03 1.64e+01 bond pdb=" C3' DT J 43 " pdb=" C2' DT J 43 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.57e+01 bond pdb=" C3' DG I 89 " pdb=" C2' DG I 89 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.52e+01 bond pdb=" C3' DG I 74 " pdb=" O3' DG I 74 " ideal model delta sigma weight residual 1.435 1.385 0.050 1.30e-02 5.92e+03 1.49e+01 ... (remaining 11537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 14773 1.54 - 3.07: 1624 3.07 - 4.61: 198 4.61 - 6.14: 33 6.14 - 7.68: 9 Bond angle restraints: 16637 Sorted by residual: angle pdb=" O4' DA I 113 " pdb=" C1' DA I 113 " pdb=" N9 DA I 113 " ideal model delta sigma weight residual 108.00 104.02 3.98 7.00e-01 2.04e+00 3.23e+01 angle pdb=" O4' DG I 86 " pdb=" C1' DG I 86 " pdb=" N9 DG I 86 " ideal model delta sigma weight residual 108.00 111.97 -3.97 7.00e-01 2.04e+00 3.21e+01 angle pdb=" O4' DA J 76 " pdb=" C1' DA J 76 " pdb=" N9 DA J 76 " ideal model delta sigma weight residual 108.00 111.82 -3.82 7.00e-01 2.04e+00 2.98e+01 angle pdb=" O4' DA I 31 " pdb=" C1' DA I 31 " pdb=" N9 DA I 31 " ideal model delta sigma weight residual 108.00 104.29 3.71 7.00e-01 2.04e+00 2.80e+01 angle pdb=" O5' DC I 9 " pdb=" C5' DC I 9 " pdb=" C4' DC I 9 " ideal model delta sigma weight residual 109.40 113.36 -3.96 8.00e-01 1.56e+00 2.46e+01 ... (remaining 16632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.69: 4776 30.69 - 61.37: 1489 61.37 - 92.05: 46 92.05 - 122.74: 8 122.74 - 153.42: 4 Dihedral angle restraints: 6323 sinusoidal: 4214 harmonic: 2109 Sorted by residual: dihedral pdb=" C4' DT I 120 " pdb=" C3' DT I 120 " pdb=" O3' DT I 120 " pdb=" P DC I 121 " ideal model delta sinusoidal sigma weight residual 220.00 66.58 153.42 1 3.50e+01 8.16e-04 1.48e+01 dihedral pdb=" C4' DT J 114 " pdb=" C3' DT J 114 " pdb=" O3' DT J 114 " pdb=" P DC J 115 " ideal model delta sinusoidal sigma weight residual 220.00 76.89 143.11 1 3.50e+01 8.16e-04 1.41e+01 dihedral pdb=" C4' DC I 100 " pdb=" C3' DC I 100 " pdb=" O3' DC I 100 " pdb=" P DT I 101 " ideal model delta sinusoidal sigma weight residual 220.00 94.95 125.05 1 3.50e+01 8.16e-04 1.23e+01 ... (remaining 6320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1300 0.062 - 0.123: 480 0.123 - 0.185: 106 0.185 - 0.246: 14 0.246 - 0.308: 2 Chirality restraints: 1902 Sorted by residual: chirality pdb=" C3' DT J 114 " pdb=" C4' DT J 114 " pdb=" O3' DT J 114 " pdb=" C2' DT J 114 " both_signs ideal model delta sigma weight residual False -2.73 -2.42 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C3' DC I 100 " pdb=" C4' DC I 100 " pdb=" O3' DC I 100 " pdb=" C2' DC I 100 " both_signs ideal model delta sigma weight residual False -2.73 -2.48 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C3' DC I 37 " pdb=" C4' DC I 37 " pdb=" O3' DC I 37 " pdb=" C2' DC I 37 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1899 not shown) Planarity restraints: 1240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 9 " -0.036 2.00e-02 2.50e+03 1.88e-02 7.92e+00 pdb=" N1 DC I 9 " 0.039 2.00e-02 2.50e+03 pdb=" C2 DC I 9 " -0.005 2.00e-02 2.50e+03 pdb=" O2 DC I 9 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC I 9 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC I 9 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC I 9 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DC I 9 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DC I 9 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 9 " -0.024 2.00e-02 2.50e+03 1.78e-02 7.11e+00 pdb=" N1 DC J 9 " 0.044 2.00e-02 2.50e+03 pdb=" C2 DC J 9 " -0.017 2.00e-02 2.50e+03 pdb=" O2 DC J 9 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DC J 9 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC J 9 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC J 9 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DC J 9 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC J 9 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 31 " -0.038 2.00e-02 2.50e+03 1.60e-02 7.00e+00 pdb=" N9 DA I 31 " 0.029 2.00e-02 2.50e+03 pdb=" C8 DA I 31 " 0.014 2.00e-02 2.50e+03 pdb=" N7 DA I 31 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 31 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 31 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 31 " -0.013 2.00e-02 2.50e+03 pdb=" N1 DA I 31 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 31 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DA I 31 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DA I 31 " 0.004 2.00e-02 2.50e+03 ... (remaining 1237 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 186 2.63 - 3.20: 9662 3.20 - 3.76: 21647 3.76 - 4.33: 27367 4.33 - 4.90: 38963 Nonbonded interactions: 97825 Sorted by model distance: nonbonded pdb=" OG SER E 69 " pdb=" NH1 ARG E 73 " model vdw 2.062 3.120 nonbonded pdb=" N ASN D 55 " pdb=" OP1 DA I 12 " model vdw 2.134 3.120 nonbonded pdb=" OG SER C 41 " pdb=" OP1 DG J 98 " model vdw 2.178 3.040 nonbonded pdb=" OH TYR F 68 " pdb=" OE2 GLU H 75 " model vdw 2.203 3.040 nonbonded pdb=" N2 DG I 114 " pdb=" O2 DT J 13 " model vdw 2.210 3.120 ... (remaining 97820 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 'E' and resid 51 through 140) } ncs_group { reference = (chain 'B' and (resid 20 through 96 or (resid 97 and (name N or name CA or name \ C )))) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 7 through 65 or resid 67 through 125)) selection = (chain 'J' and (resid 1 through 59 or resid 61 through 119)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.520 Find NCS groups from input model: 0.140 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 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 : 0.010 0.083 11542 Z= 0.697 Angle : 0.987 7.680 16637 Z= 0.767 Chirality : 0.065 0.308 1902 Planarity : 0.005 0.042 1240 Dihedral : 28.860 153.423 4955 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.29), residues: 711 helix: -0.22 (0.21), residues: 513 sheet: None (None), residues: 0 loop : -2.04 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 64 TYR 0.020 0.003 TYR C 47 PHE 0.025 0.004 PHE C 94 HIS 0.016 0.002 HIS G 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00978 / 0.70 (11542) covalent geometry : angle 0.98679 / 0.77 (16637) hydrogen bonds : bond 0.09313 / 6.12 ( 707) hydrogen bonds : angle 4.46578 / 3.19 ( 1794) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 138 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7769 (mp0) REVERT: B 35 ARG cc_start: 0.8081 (mtt-85) cc_final: 0.7724 (mtt90) REVERT: D 78 ASN cc_start: 0.8833 (t0) cc_final: 0.8304 (t0) REVERT: D 82 ILE cc_start: 0.9136 (mt) cc_final: 0.8678 (mt) REVERT: F 31 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.8033 (mmm160) REVERT: F 87 LYS cc_start: 0.8948 (ttpt) cc_final: 0.8581 (ttmt) REVERT: H 51 LEU cc_start: 0.7360 (pp) cc_final: 0.7109 (pp) REVERT: C 96 ASN cc_start: 0.8080 (p0) cc_final: 0.7802 (p0) REVERT: C 101 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7940 (mt-10) REVERT: G 85 ARG cc_start: 0.7539 (mtt180) cc_final: 0.7337 (mtt180) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1212 time to fit residues: 19.6073 Evaluate side-chains 100 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 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 = 0.4197 r_free = 0.4197 target = 0.180936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.123298 restraints weight = 14713.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.123925 restraints weight = 9932.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.124463 restraints weight = 9241.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.124962 restraints weight = 8792.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.125144 restraints weight = 8775.712| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 11542 Z= 0.166 Angle : 0.770 8.589 16637 Z= 0.429 Chirality : 0.055 0.387 1902 Planarity : 0.006 0.065 1240 Dihedral : 32.659 162.235 3513 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.62 % Allowed : 14.08 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.28), residues: 711 helix: 0.57 (0.20), residues: 521 sheet: None (None), residues: 0 loop : -1.40 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 132 TYR 0.021 0.002 TYR E 55 PHE 0.031 0.002 PHE G 60 HIS 0.014 0.002 HIS G 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.17 (11542) covalent geometry : angle 0.76956 / 0.43 (16637) hydrogen bonds : bond 0.05325 / 3.61 ( 707) hydrogen bonds : angle 3.69013 / 2.63 ( 1794) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 31 ARG cc_start: 0.8315 (mmm-85) cc_final: 0.8028 (mmm160) REVERT: F 51 ARG cc_start: 0.8211 (mtt180) cc_final: 0.7939 (mtt-85) REVERT: F 87 LYS cc_start: 0.8871 (ttpt) cc_final: 0.8481 (ttmt) REVERT: H 84 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7907 (mmtt) REVERT: C 96 ASN cc_start: 0.8089 (p0) cc_final: 0.7803 (p0) REVERT: C 101 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7857 (mt-10) outliers start: 10 outliers final: 2 residues processed: 118 average time/residue: 0.1064 time to fit residues: 16.7928 Evaluate side-chains 99 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 82 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 78 optimal weight: 40.0000 chunk 74 optimal weight: 30.0000 chunk 53 optimal weight: 0.7980 chunk 90 optimal weight: 50.0000 chunk 2 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 88 optimal weight: 30.0000 chunk 67 optimal weight: 4.9990 chunk 91 optimal weight: 50.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 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 = 0.4181 r_free = 0.4181 target = 0.179490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.122192 restraints weight = 14940.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.123419 restraints weight = 10357.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124097 restraints weight = 9707.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.124595 restraints weight = 8542.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.124742 restraints weight = 8275.752| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 11542 Z= 0.194 Angle : 0.723 7.784 16637 Z= 0.406 Chirality : 0.051 0.333 1902 Planarity : 0.005 0.048 1240 Dihedral : 32.490 175.416 3513 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.07 % Allowed : 16.50 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.29), residues: 711 helix: 0.83 (0.21), residues: 524 sheet: None (None), residues: 0 loop : -1.16 (0.42), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 132 TYR 0.020 0.002 TYR E 55 PHE 0.015 0.002 PHE G 60 HIS 0.011 0.002 HIS G 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (11542) covalent geometry : angle 0.72267 / 0.41 (16637) hydrogen bonds : bond 0.04932 / 3.36 ( 707) hydrogen bonds : angle 3.50467 / 2.49 ( 1794) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 112 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7080 (mt-10) REVERT: E 62 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8113 (mm) REVERT: F 31 ARG cc_start: 0.8303 (mmm-85) cc_final: 0.8035 (mmm160) REVERT: F 51 ARG cc_start: 0.8203 (mtt180) cc_final: 0.7913 (mtt-85) REVERT: F 87 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8555 (ttmt) REVERT: H 84 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7896 (mmtt) REVERT: C 96 ASN cc_start: 0.8060 (p0) cc_final: 0.7797 (p0) REVERT: C 101 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7873 (mt-10) outliers start: 19 outliers final: 11 residues processed: 110 average time/residue: 0.0936 time to fit residues: 14.4327 Evaluate side-chains 104 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 82 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 75 optimal weight: 30.0000 chunk 82 optimal weight: 40.0000 chunk 9 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 89 optimal weight: 30.0000 chunk 59 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN E 44 GLN ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.181254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.123073 restraints weight = 14998.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124723 restraints weight = 10475.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.124831 restraints weight = 9437.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.125296 restraints weight = 8766.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.125862 restraints weight = 7999.637| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11542 Z= 0.153 Angle : 0.671 10.123 16637 Z= 0.382 Chirality : 0.048 0.311 1902 Planarity : 0.004 0.048 1240 Dihedral : 32.326 179.247 3513 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.27 % Allowed : 17.96 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.30), residues: 711 helix: 1.24 (0.21), residues: 520 sheet: None (None), residues: 0 loop : -1.13 (0.41), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 36 TYR 0.013 0.001 TYR E 55 PHE 0.013 0.002 PHE G 60 HIS 0.009 0.002 HIS G 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 (11542) covalent geometry : angle 0.67099 / 0.38 (16637) hydrogen bonds : bond 0.04471 / 3.05 ( 707) hydrogen bonds : angle 3.36974 / 2.39 ( 1794) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: D 119 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8098 (tmmt) REVERT: E 62 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7868 (mm) REVERT: F 87 LYS cc_start: 0.8863 (ttpt) cc_final: 0.8504 (ttmt) REVERT: H 41 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8012 (tm-30) REVERT: H 84 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7868 (mmtt) REVERT: C 96 ASN cc_start: 0.8064 (p0) cc_final: 0.7811 (p0) REVERT: C 101 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7831 (mt-10) REVERT: G 81 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8263 (tp) outliers start: 14 outliers final: 8 residues processed: 106 average time/residue: 0.1004 time to fit residues: 14.4305 Evaluate side-chains 104 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 87 optimal weight: 30.0000 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 81 optimal weight: 40.0000 chunk 10 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 75 optimal weight: 30.0000 chunk 14 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.181703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.124240 restraints weight = 14978.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.126310 restraints weight = 10049.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126459 restraints weight = 8910.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126796 restraints weight = 8461.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.127291 restraints weight = 7649.373| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11542 Z= 0.145 Angle : 0.653 8.587 16637 Z= 0.374 Chirality : 0.046 0.297 1902 Planarity : 0.005 0.081 1240 Dihedral : 32.199 179.108 3513 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.91 % Allowed : 18.45 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.30), residues: 711 helix: 1.50 (0.21), residues: 520 sheet: None (None), residues: 0 loop : -1.09 (0.41), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 132 TYR 0.010 0.001 TYR E 55 PHE 0.019 0.001 PHE G 60 HIS 0.008 0.002 HIS G 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 (11542) covalent geometry : angle 0.65320 / 0.37 (16637) hydrogen bonds : bond 0.04349 / 2.96 ( 707) hydrogen bonds : angle 3.26292 / 2.31 ( 1794) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: D 119 LYS cc_start: 0.8640 (ttmt) cc_final: 0.8148 (tmmt) REVERT: F 87 LYS cc_start: 0.8854 (ttpt) cc_final: 0.8494 (ttmt) REVERT: H 41 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7972 (tm-30) REVERT: H 84 LYS cc_start: 0.8162 (mmtt) cc_final: 0.7774 (mmtt) REVERT: C 96 ASN cc_start: 0.8025 (p0) cc_final: 0.7772 (p0) REVERT: C 101 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7792 (mt-10) REVERT: G 81 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8260 (tp) outliers start: 18 outliers final: 13 residues processed: 108 average time/residue: 0.0834 time to fit residues: 12.8095 Evaluate side-chains 105 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 76 optimal weight: 30.0000 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 30.0000 chunk 68 optimal weight: 50.0000 chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.181246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.124322 restraints weight = 15032.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.125177 restraints weight = 10345.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.125739 restraints weight = 9546.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126329 restraints weight = 8747.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126539 restraints weight = 8402.243| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11542 Z= 0.163 Angle : 0.654 11.674 16637 Z= 0.372 Chirality : 0.046 0.264 1902 Planarity : 0.005 0.057 1240 Dihedral : 32.185 179.755 3513 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.40 % Allowed : 19.26 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.30), residues: 711 helix: 1.51 (0.21), residues: 520 sheet: None (None), residues: 0 loop : -1.08 (0.41), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 36 TYR 0.011 0.001 TYR E 102 PHE 0.014 0.001 PHE G 60 HIS 0.009 0.002 HIS G 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (11542) covalent geometry : angle 0.65403 / 0.37 (16637) hydrogen bonds : bond 0.04348 / 2.96 ( 707) hydrogen bonds : angle 3.24528 / 2.29 ( 1794) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.221 Fit side-chains REVERT: D 119 LYS cc_start: 0.8648 (ttmt) cc_final: 0.8084 (tmmt) REVERT: F 31 ARG cc_start: 0.8262 (mmm-85) cc_final: 0.8034 (mmm160) REVERT: F 51 ARG cc_start: 0.8593 (mtt-85) cc_final: 0.8367 (mtt-85) REVERT: F 87 LYS cc_start: 0.8868 (ttpt) cc_final: 0.8489 (ttmt) REVERT: H 84 LYS cc_start: 0.8114 (mmtt) cc_final: 0.7670 (mmtt) REVERT: C 96 ASN cc_start: 0.8043 (p0) cc_final: 0.7772 (p0) REVERT: C 101 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7708 (mt-10) REVERT: G 81 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8257 (tp) outliers start: 21 outliers final: 17 residues processed: 106 average time/residue: 0.0988 time to fit residues: 14.4182 Evaluate side-chains 108 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 76 optimal weight: 30.0000 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 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 = 0.4191 r_free = 0.4191 target = 0.180783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123483 restraints weight = 15093.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.124469 restraints weight = 10411.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.124933 restraints weight = 9508.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.125561 restraints weight = 8719.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125779 restraints weight = 8315.517| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11542 Z= 0.169 Angle : 0.646 8.942 16637 Z= 0.368 Chirality : 0.045 0.265 1902 Planarity : 0.005 0.055 1240 Dihedral : 32.147 179.245 3513 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.56 % Allowed : 19.58 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.30), residues: 711 helix: 1.45 (0.21), residues: 521 sheet: None (None), residues: 0 loop : -1.11 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 36 TYR 0.012 0.001 TYR E 102 PHE 0.016 0.001 PHE G 60 HIS 0.008 0.002 HIS G 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (11542) covalent geometry : angle 0.64578 / 0.37 (16637) hydrogen bonds : bond 0.04323 / 2.94 ( 707) hydrogen bonds : angle 3.28977 / 2.33 ( 1794) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.282 Fit side-chains REVERT: D 119 LYS cc_start: 0.8646 (ttmt) cc_final: 0.8087 (tmmt) REVERT: F 87 LYS cc_start: 0.8875 (ttpt) cc_final: 0.8495 (ttmt) REVERT: H 84 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7773 (mmtt) REVERT: C 62 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7407 (mm-30) REVERT: C 96 ASN cc_start: 0.8034 (p0) cc_final: 0.7792 (p0) REVERT: C 101 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7717 (mt-10) REVERT: G 81 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8269 (tp) outliers start: 22 outliers final: 16 residues processed: 105 average time/residue: 0.0960 time to fit residues: 14.0904 Evaluate side-chains 104 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 45 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 30.0000 chunk 42 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 84 optimal weight: 40.0000 chunk 40 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 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 = 0.4189 r_free = 0.4189 target = 0.180621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.123195 restraints weight = 15042.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.124947 restraints weight = 9982.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.125116 restraints weight = 9101.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125495 restraints weight = 8501.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.126044 restraints weight = 7719.319| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11542 Z= 0.173 Angle : 0.647 13.862 16637 Z= 0.366 Chirality : 0.044 0.265 1902 Planarity : 0.004 0.045 1240 Dihedral : 32.066 179.126 3513 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.24 % Allowed : 19.58 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.30), residues: 711 helix: 1.48 (0.21), residues: 521 sheet: None (None), residues: 0 loop : -1.07 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 36 TYR 0.017 0.002 TYR E 55 PHE 0.012 0.002 PHE G 60 HIS 0.007 0.001 HIS G 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (11542) covalent geometry : angle 0.64662 / 0.37 (16637) hydrogen bonds : bond 0.04309 / 2.93 ( 707) hydrogen bonds : angle 3.28485 / 2.32 ( 1794) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.320 Fit side-chains REVERT: D 119 LYS cc_start: 0.8600 (ttmt) cc_final: 0.8022 (tmmt) REVERT: F 87 LYS cc_start: 0.8867 (ttpt) cc_final: 0.8482 (ttmt) REVERT: H 84 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7654 (mmtt) REVERT: C 62 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7488 (mm-30) REVERT: C 96 ASN cc_start: 0.8053 (p0) cc_final: 0.7821 (p0) REVERT: C 101 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7742 (mt-10) outliers start: 20 outliers final: 16 residues processed: 105 average time/residue: 0.1025 time to fit residues: 14.9259 Evaluate side-chains 105 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 45 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.181827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.124858 restraints weight = 14907.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125894 restraints weight = 10385.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.126250 restraints weight = 9563.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.126734 restraints weight = 8822.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.127256 restraints weight = 8021.937| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11542 Z= 0.153 Angle : 0.616 10.271 16637 Z= 0.355 Chirality : 0.043 0.267 1902 Planarity : 0.005 0.065 1240 Dihedral : 31.872 179.981 3513 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.91 % Allowed : 19.74 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.30), residues: 711 helix: 1.61 (0.21), residues: 520 sheet: None (None), residues: 0 loop : -1.20 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 51 TYR 0.012 0.001 TYR E 102 PHE 0.014 0.002 PHE G 60 HIS 0.006 0.001 HIS G 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (11542) covalent geometry : angle 0.61572 / 0.36 (16637) hydrogen bonds : bond 0.04198 / 2.88 ( 707) hydrogen bonds : angle 3.25117 / 2.30 ( 1794) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.276 Fit side-chains REVERT: D 119 LYS cc_start: 0.8657 (ttmt) cc_final: 0.8050 (tmmt) REVERT: F 87 LYS cc_start: 0.8847 (ttpt) cc_final: 0.8475 (ttmt) REVERT: H 84 LYS cc_start: 0.8082 (mmtt) cc_final: 0.7610 (mmtt) REVERT: C 62 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7470 (mm-30) REVERT: C 101 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7682 (mt-10) outliers start: 18 outliers final: 14 residues processed: 104 average time/residue: 0.0902 time to fit residues: 13.3164 Evaluate side-chains 104 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 42 optimal weight: 6.9990 chunk 71 optimal weight: 40.0000 chunk 27 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 88 optimal weight: 30.0000 chunk 67 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 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 = 0.182131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.125409 restraints weight = 14992.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126015 restraints weight = 10384.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126641 restraints weight = 9516.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.127270 restraints weight = 8637.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.127534 restraints weight = 8246.778| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11542 Z= 0.146 Angle : 0.615 11.794 16637 Z= 0.355 Chirality : 0.043 0.268 1902 Planarity : 0.004 0.045 1240 Dihedral : 31.746 179.464 3513 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.27 % Allowed : 21.20 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.29), residues: 711 helix: 1.69 (0.21), residues: 521 sheet: None (None), residues: 0 loop : -1.07 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 36 TYR 0.015 0.001 TYR E 55 PHE 0.008 0.001 PHE A 68 HIS 0.008 0.001 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (11542) covalent geometry : angle 0.61535 / 0.36 (16637) hydrogen bonds : bond 0.04182 / 2.87 ( 707) hydrogen bonds : angle 3.23114 / 2.29 ( 1794) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.168 Fit side-chains REVERT: D 119 LYS cc_start: 0.8622 (ttmt) cc_final: 0.8085 (tmmt) REVERT: F 87 LYS cc_start: 0.8828 (ttpt) cc_final: 0.8455 (ttmt) REVERT: H 84 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7575 (mmtt) REVERT: H 104 GLU cc_start: 0.7516 (tp30) cc_final: 0.6931 (tp30) REVERT: H 107 ARG cc_start: 0.7850 (ttp80) cc_final: 0.7410 (tmm-80) REVERT: C 62 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7478 (mm-30) REVERT: C 96 ASN cc_start: 0.8053 (p0) cc_final: 0.7843 (p0) outliers start: 14 outliers final: 13 residues processed: 99 average time/residue: 0.0895 time to fit residues: 12.3718 Evaluate side-chains 100 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 73 optimal weight: 30.0000 chunk 72 optimal weight: 20.0000 chunk 2 optimal weight: 0.7980 chunk 91 optimal weight: 50.0000 chunk 49 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.180184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123805 restraints weight = 15114.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123857 restraints weight = 11092.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.125052 restraints weight = 10170.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.125499 restraints weight = 8672.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.125872 restraints weight = 8327.612| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11542 Z= 0.216 Angle : 0.658 10.578 16637 Z= 0.371 Chirality : 0.045 0.268 1902 Planarity : 0.005 0.044 1240 Dihedral : 31.845 179.937 3513 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.10 % Allowed : 21.84 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.29), residues: 711 helix: 1.40 (0.21), residues: 521 sheet: None (None), residues: 0 loop : -1.07 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 51 TYR 0.015 0.002 TYR E 102 PHE 0.008 0.002 PHE G 60 HIS 0.008 0.002 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.22 (11542) covalent geometry : angle 0.65786 / 0.37 (16637) hydrogen bonds : bond 0.04491 / 3.07 ( 707) hydrogen bonds : angle 3.33265 / 2.36 ( 1794) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1200.31 seconds wall clock time: 21 minutes 38.12 seconds (1298.12 seconds total)