Starting phenix.real_space_refine on Fri Jul 3 02:27:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v90_31806/07_2026/7v90_31806.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v90_31806/07_2026/7v90_31806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v90_31806/07_2026/7v90_31806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v90_31806/07_2026/7v90_31806.map" model { file = "/net/cci-nas-00/data/ceres_data/7v90_31806/07_2026/7v90_31806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v90_31806/07_2026/7v90_31806.cif" } resolution = 3.5 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= 0.005 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 288 5.49 5 S 14 5.16 5 C 6737 2.51 5 N 2288 2.21 5 O 2821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12148 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 824 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 783 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "E" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 773 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "I" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 3067 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2872 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 2.33, per 1000 atoms: 0.19 Number of scatterers: 12148 At special positions: 0 Unit cell: (115.83, 113.256, 124.41, 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 14 16.00 P 288 15.00 O 2821 8.00 N 2288 7.00 C 6737 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: 0.81 Conformation dependent library (CDL) restraints added in 154.1 milliseconds 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1458 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 7 sheets defined 69.4% alpha, 2.3% beta 123 base pairs and 249 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 64 through 75 removed outlier: 3.633A pdb=" N ALA A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.575A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.977A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 120 through 126' Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.568A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 27 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.796A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.794A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.467A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 95 removed outlier: 4.057A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 90 through 95' Processing helix chain 'D' and resid 35 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.699A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.566A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.667A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.745A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.644A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 76 Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.680A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.597A pdb=" N LYS H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.759A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.720A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.004A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.447A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.439A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102 removed outlier: 7.007A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.102A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.665A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 380 hydrogen bonds defined for protein. 1134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 306 hydrogen bonds 612 hydrogen bond angles 0 basepair planarities 123 basepair parallelities 249 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1411 1.32 - 1.44: 4779 1.44 - 1.56: 6161 1.56 - 1.69: 576 1.69 - 1.81: 24 Bond restraints: 12951 Sorted by residual: bond pdb=" N ASP C 90 " pdb=" CA ASP C 90 " ideal model delta sigma weight residual 1.456 1.529 -0.074 1.25e-02 6.40e+03 3.47e+01 bond pdb=" CA SER D 35 " pdb=" CB SER D 35 " ideal model delta sigma weight residual 1.535 1.480 0.055 1.58e-02 4.01e+03 1.19e+01 bond pdb=" O3' DG I 12 " pdb=" P DG I 13 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.50e-02 4.44e+03 1.15e+01 bond pdb=" C3' DA J 51 " pdb=" C2' DA J 51 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DA J -16 " pdb=" C2' DA J -16 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 ... (remaining 12946 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 17947 2.16 - 4.33: 731 4.33 - 6.49: 33 6.49 - 8.65: 5 8.65 - 10.81: 2 Bond angle restraints: 18718 Sorted by residual: angle pdb=" C TYR D 34 " pdb=" CA TYR D 34 " pdb=" CB TYR D 34 " ideal model delta sigma weight residual 112.12 103.64 8.48 1.50e+00 4.44e-01 3.20e+01 angle pdb=" N LEU A 126 " pdb=" CA LEU A 126 " pdb=" C LEU A 126 " ideal model delta sigma weight residual 112.87 106.38 6.49 1.20e+00 6.94e-01 2.92e+01 angle pdb=" N ARG A 128 " pdb=" CA ARG A 128 " pdb=" C ARG A 128 " ideal model delta sigma weight residual 110.80 99.99 10.81 2.13e+00 2.20e-01 2.58e+01 angle pdb=" N ASP C 90 " pdb=" CA ASP C 90 " pdb=" C ASP C 90 " ideal model delta sigma weight residual 110.35 117.18 -6.83 1.36e+00 5.41e-01 2.52e+01 angle pdb=" N PHE F 100 " pdb=" CA PHE F 100 " pdb=" C PHE F 100 " ideal model delta sigma weight residual 113.18 107.27 5.91 1.21e+00 6.83e-01 2.38e+01 ... (remaining 18713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.87: 5636 30.87 - 61.74: 1444 61.74 - 92.61: 24 92.61 - 123.48: 0 123.48 - 154.35: 1 Dihedral angle restraints: 7105 sinusoidal: 4844 harmonic: 2261 Sorted by residual: dihedral pdb=" N ASP C 90 " pdb=" C ASP C 90 " pdb=" CA ASP C 90 " pdb=" CB ASP C 90 " ideal model delta harmonic sigma weight residual 122.80 135.60 -12.80 0 2.50e+00 1.60e-01 2.62e+01 dihedral pdb=" C ASP C 90 " pdb=" N ASP C 90 " pdb=" CA ASP C 90 " pdb=" CB ASP C 90 " ideal model delta harmonic sigma weight residual -122.60 -133.28 10.68 0 2.50e+00 1.60e-01 1.83e+01 dihedral pdb=" C ARG C 20 " pdb=" N ARG C 20 " pdb=" CA ARG C 20 " pdb=" CB ARG C 20 " ideal model delta harmonic sigma weight residual -122.60 -133.22 10.62 0 2.50e+00 1.60e-01 1.81e+01 ... (remaining 7102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1891 0.080 - 0.160: 209 0.160 - 0.240: 15 0.240 - 0.320: 7 0.320 - 0.400: 1 Chirality restraints: 2123 Sorted by residual: chirality pdb=" CA ASP C 90 " pdb=" N ASP C 90 " pdb=" C ASP C 90 " pdb=" CB ASP C 90 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA TYR D 34 " pdb=" N TYR D 34 " pdb=" C TYR D 34 " pdb=" CB TYR D 34 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA ARG C 20 " pdb=" N ARG C 20 " pdb=" C ARG C 20 " pdb=" CB ARG C 20 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 2120 not shown) Planarity restraints: 1365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 90 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C ASP C 90 " -0.060 2.00e-02 2.50e+03 pdb=" O ASP C 90 " 0.022 2.00e-02 2.50e+03 pdb=" N GLU C 91 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 88 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C ARG C 88 " 0.042 2.00e-02 2.50e+03 pdb=" O ARG C 88 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN C 89 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 125 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C GLN A 125 " -0.028 2.00e-02 2.50e+03 pdb=" O GLN A 125 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 126 " 0.009 2.00e-02 2.50e+03 ... (remaining 1362 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1458 2.75 - 3.29: 10271 3.29 - 3.83: 22498 3.83 - 4.36: 25965 4.36 - 4.90: 39112 Nonbonded interactions: 99304 Sorted by model distance: nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.219 3.040 nonbonded pdb=" O GLU D 102 " pdb=" ND1 HIS D 106 " model vdw 2.303 3.120 nonbonded pdb=" O ILE A 119 " pdb=" OG SER B 47 " model vdw 2.398 3.040 nonbonded pdb=" N2 DG I -28 " pdb=" N3 DC J 28 " model vdw 2.416 3.200 nonbonded pdb=" NH1 ARG G 32 " pdb=" OP1 DC J -44 " model vdw 2.430 3.120 ... (remaining 99299 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 36 through 134 or (resid 135 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 24 through 121) selection = chain 'H' } 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: 0.970 Set stop_for_unknowns flag: 0.010 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.650 Find NCS groups from input model: 0.170 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 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 : 0.006 0.074 12951 Z= 0.559 Angle : 0.839 10.814 18718 Z= 0.717 Chirality : 0.052 0.400 2123 Planarity : 0.003 0.035 1365 Dihedral : 26.094 154.348 5647 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.71 % Favored : 94.77 % Rotamer: Outliers : 4.01 % Allowed : 5.08 % Favored : 90.91 % Cbeta Deviations : 0.41 % 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: -0.16 (0.28), residues: 765 helix: 0.89 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -2.20 (0.30), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 131 TYR 0.015 0.001 TYR D 34 PHE 0.021 0.001 PHE F 100 HIS 0.004 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.56 (12951) covalent geometry : angle 0.83851 / 0.72 (18718) hydrogen bonds : bond 0.12146 / 7.96 ( 686) hydrogen bonds : angle 4.20261 / 3.11 ( 1746) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8084 (mtpp) cc_final: 0.7696 (mttp) REVERT: C 15 LYS cc_start: 0.7457 (mtpp) cc_final: 0.7038 (tttp) REVERT: D 30 ARG cc_start: 0.5004 (ptm-80) cc_final: 0.4200 (mtp85) REVERT: F 35 ARG cc_start: 0.8054 (mtt-85) cc_final: 0.7353 (mtm-85) REVERT: G 15 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7554 (tttt) REVERT: H 25 LYS cc_start: 0.3299 (OUTLIER) cc_final: 0.2115 (ptmt) outliers start: 26 outliers final: 4 residues processed: 141 average time/residue: 0.1966 time to fit residues: 34.1452 Evaluate side-chains 70 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain H residue 25 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 30.0000 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS C 84 GLN D 44 GLN D 46 HIS D 60 ASN F 25 ASN H 44 GLN H 92 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.181903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.139844 restraints weight = 15353.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.139141 restraints weight = 24366.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.139544 restraints weight = 23255.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.139729 restraints weight = 19277.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.140348 restraints weight = 18024.613| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12951 Z= 0.144 Angle : 0.570 6.057 18718 Z= 0.354 Chirality : 0.040 0.290 2123 Planarity : 0.004 0.037 1365 Dihedral : 29.774 155.977 4091 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.27 % Favored : 96.47 % Rotamer: Outliers : 2.00 % Allowed : 8.78 % Favored : 89.21 % 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: 765 helix: 1.86 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -2.12 (0.32), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 77 TYR 0.017 0.001 TYR D 34 PHE 0.006 0.001 PHE F 61 HIS 0.005 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.14 (12951) covalent geometry : angle 0.56973 / 0.35 (18718) hydrogen bonds : bond 0.05666 / 4.00 ( 686) hydrogen bonds : angle 2.56842 / 1.87 ( 1746) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: D 28 ARG cc_start: 0.4686 (OUTLIER) cc_final: 0.4485 (ptp-170) REVERT: D 30 ARG cc_start: 0.6038 (ptm-80) cc_final: 0.5210 (mtp180) REVERT: F 35 ARG cc_start: 0.7866 (mtt-85) cc_final: 0.7605 (mtm110) REVERT: G 15 LYS cc_start: 0.8256 (mtpt) cc_final: 0.7914 (tttt) REVERT: H 98 LEU cc_start: 0.8796 (mm) cc_final: 0.8550 (mm) outliers start: 13 outliers final: 6 residues processed: 84 average time/residue: 0.1457 time to fit residues: 16.0158 Evaluate side-chains 72 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 84 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 81 optimal weight: 30.0000 chunk 34 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN F 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.167432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.122822 restraints weight = 14978.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.121529 restraints weight = 24381.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.122374 restraints weight = 22866.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.122551 restraints weight = 18402.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.122782 restraints weight = 19468.518| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12951 Z= 0.198 Angle : 0.648 6.824 18718 Z= 0.378 Chirality : 0.044 0.315 2123 Planarity : 0.005 0.050 1365 Dihedral : 30.466 159.797 4077 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.92 % Favored : 95.82 % Rotamer: Outliers : 2.16 % Allowed : 8.63 % Favored : 89.21 % 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: 1.32 (0.30), residues: 765 helix: 2.03 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.98 (0.33), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 128 TYR 0.017 0.002 TYR A 54 PHE 0.020 0.003 PHE H 62 HIS 0.011 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.20 (12951) covalent geometry : angle 0.64808 / 0.38 (18718) hydrogen bonds : bond 0.08164 / 5.50 ( 686) hydrogen bonds : angle 2.89210 / 2.07 ( 1746) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9232 (m-80) cc_final: 0.8944 (m-80) REVERT: A 109 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8213 (mp) REVERT: C 75 LYS cc_start: 0.8162 (mttm) cc_final: 0.7954 (mttp) REVERT: D 30 ARG cc_start: 0.5920 (ptm-80) cc_final: 0.5041 (mtp180) REVERT: F 35 ARG cc_start: 0.7931 (mtt-85) cc_final: 0.7451 (mtm110) REVERT: H 96 ARG cc_start: 0.7837 (mtp180) cc_final: 0.7486 (mtm180) outliers start: 14 outliers final: 9 residues processed: 88 average time/residue: 0.1388 time to fit residues: 16.2755 Evaluate side-chains 78 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 84 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 30.0000 chunk 60 optimal weight: 3.9990 chunk 30 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.167170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.122717 restraints weight = 14918.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.120838 restraints weight = 26120.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.121893 restraints weight = 25839.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.122207 restraints weight = 19298.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.122287 restraints weight = 20668.292| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12951 Z= 0.159 Angle : 0.570 5.652 18718 Z= 0.341 Chirality : 0.040 0.313 2123 Planarity : 0.004 0.042 1365 Dihedral : 30.421 161.512 4077 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.40 % Favored : 96.47 % Rotamer: Outliers : 2.16 % Allowed : 9.86 % Favored : 87.98 % 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: 1.79 (0.30), residues: 765 helix: 2.41 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.92 (0.34), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 20 TYR 0.013 0.001 TYR F 51 PHE 0.012 0.002 PHE F 100 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (12951) covalent geometry : angle 0.56978 / 0.34 (18718) hydrogen bonds : bond 0.06842 / 4.63 ( 686) hydrogen bonds : angle 2.71016 / 1.93 ( 1746) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9203 (m-80) cc_final: 0.8995 (m-80) REVERT: C 74 LYS cc_start: 0.7410 (mtmp) cc_final: 0.6900 (mmmt) REVERT: D 30 ARG cc_start: 0.5933 (ptm-80) cc_final: 0.5093 (mtp180) REVERT: F 35 ARG cc_start: 0.7927 (mtt-85) cc_final: 0.7444 (mtm110) REVERT: H 81 ASN cc_start: 0.8344 (m-40) cc_final: 0.8080 (m-40) REVERT: H 96 ARG cc_start: 0.7783 (mtp180) cc_final: 0.7409 (mtm180) outliers start: 14 outliers final: 14 residues processed: 80 average time/residue: 0.1260 time to fit residues: 13.7008 Evaluate side-chains 77 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 84 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 86 optimal weight: 30.0000 chunk 20 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.167912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.123841 restraints weight = 14941.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.121890 restraints weight = 26952.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.122868 restraints weight = 25993.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.123281 restraints weight = 19401.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.123756 restraints weight = 18484.924| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12951 Z= 0.136 Angle : 0.536 5.424 18718 Z= 0.325 Chirality : 0.039 0.312 2123 Planarity : 0.003 0.035 1365 Dihedral : 30.373 161.424 4077 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.01 % Favored : 96.86 % Rotamer: Outliers : 2.31 % Allowed : 10.79 % Favored : 86.90 % 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: 2.11 (0.30), residues: 765 helix: 2.67 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.85 (0.34), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 20 TYR 0.017 0.001 TYR G 39 PHE 0.010 0.001 PHE H 62 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.14 (12951) covalent geometry : angle 0.53617 / 0.32 (18718) hydrogen bonds : bond 0.06225 / 4.22 ( 686) hydrogen bonds : angle 2.62481 / 1.87 ( 1746) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9190 (m-80) cc_final: 0.8966 (m-80) REVERT: C 74 LYS cc_start: 0.7475 (mtmp) cc_final: 0.6934 (mmmt) REVERT: D 30 ARG cc_start: 0.5875 (ptm-80) cc_final: 0.5097 (mtp180) REVERT: F 35 ARG cc_start: 0.7916 (mtt-85) cc_final: 0.7441 (mtm110) REVERT: H 73 GLU cc_start: 0.8624 (tp30) cc_final: 0.8410 (tp30) REVERT: H 81 ASN cc_start: 0.8254 (m-40) cc_final: 0.7941 (m-40) REVERT: H 96 ARG cc_start: 0.7785 (mtp180) cc_final: 0.7400 (mtm180) outliers start: 15 outliers final: 13 residues processed: 80 average time/residue: 0.1060 time to fit residues: 11.6919 Evaluate side-chains 79 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 80 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN G 38 ASN H 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.163891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.120158 restraints weight = 14840.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.118290 restraints weight = 26762.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.119209 restraints weight = 24137.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.119530 restraints weight = 18980.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.119986 restraints weight = 18459.745| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12951 Z= 0.179 Angle : 0.600 5.336 18718 Z= 0.349 Chirality : 0.042 0.323 2123 Planarity : 0.005 0.038 1365 Dihedral : 30.467 163.033 4077 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.58 % Favored : 95.29 % Rotamer: Outliers : 2.62 % Allowed : 11.56 % Favored : 85.82 % 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: 1.92 (0.30), residues: 765 helix: 2.53 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.82 (0.34), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 20 TYR 0.014 0.002 TYR D 34 PHE 0.016 0.002 PHE H 62 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 (12951) covalent geometry : angle 0.59970 / 0.35 (18718) hydrogen bonds : bond 0.07445 / 5.03 ( 686) hydrogen bonds : angle 2.82869 / 2.01 ( 1746) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9219 (m-80) cc_final: 0.8985 (m-80) REVERT: C 74 LYS cc_start: 0.7455 (mtmp) cc_final: 0.6867 (mmmt) REVERT: F 35 ARG cc_start: 0.7897 (mtt-85) cc_final: 0.7337 (mtm110) REVERT: H 73 GLU cc_start: 0.8649 (tp30) cc_final: 0.8400 (tp30) REVERT: H 81 ASN cc_start: 0.8427 (m-40) cc_final: 0.8183 (m-40) REVERT: H 89 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7714 (ptm-80) REVERT: H 96 ARG cc_start: 0.7750 (mtp180) cc_final: 0.7314 (mtm180) REVERT: H 109 SER cc_start: 0.8269 (t) cc_final: 0.8048 (m) outliers start: 17 outliers final: 15 residues processed: 84 average time/residue: 0.1196 time to fit residues: 13.6046 Evaluate side-chains 82 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 5 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 93 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.165961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.121355 restraints weight = 14817.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.119886 restraints weight = 24745.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.120818 restraints weight = 22210.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.120933 restraints weight = 18084.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.121266 restraints weight = 19102.172| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12951 Z= 0.133 Angle : 0.540 5.436 18718 Z= 0.325 Chirality : 0.039 0.312 2123 Planarity : 0.004 0.035 1365 Dihedral : 30.381 162.668 4077 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.93 % Allowed : 11.09 % Favored : 85.98 % 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: 2.26 (0.31), residues: 765 helix: 2.82 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.76 (0.34), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 20 TYR 0.025 0.001 TYR G 39 PHE 0.009 0.001 PHE H 62 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.13 (12951) covalent geometry : angle 0.53987 / 0.33 (18718) hydrogen bonds : bond 0.06322 / 4.27 ( 686) hydrogen bonds : angle 2.69310 / 1.92 ( 1746) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9165 (m-80) cc_final: 0.8948 (m-80) REVERT: C 74 LYS cc_start: 0.7494 (mtmp) cc_final: 0.7196 (mtmm) REVERT: F 35 ARG cc_start: 0.7959 (mtt-85) cc_final: 0.7448 (mtm110) REVERT: H 81 ASN cc_start: 0.8300 (m-40) cc_final: 0.8041 (m-40) REVERT: H 89 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7693 (ptm-80) REVERT: H 96 ARG cc_start: 0.7708 (mtp180) cc_final: 0.7272 (mtm180) outliers start: 19 outliers final: 16 residues processed: 83 average time/residue: 0.1087 time to fit residues: 12.3342 Evaluate side-chains 82 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 99 optimal weight: 30.0000 chunk 73 optimal weight: 1.9990 chunk 84 optimal weight: 30.0000 chunk 36 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 0.0370 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN G 38 ASN H 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.164376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.119084 restraints weight = 14809.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.117626 restraints weight = 24449.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.118422 restraints weight = 22619.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.118401 restraints weight = 20321.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.121800 restraints weight = 17878.637| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12951 Z= 0.165 Angle : 0.565 5.381 18718 Z= 0.334 Chirality : 0.040 0.312 2123 Planarity : 0.004 0.037 1365 Dihedral : 30.405 163.108 4077 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.93 % Allowed : 11.25 % Favored : 85.82 % 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: 2.09 (0.30), residues: 765 helix: 2.68 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.84 (0.34), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 20 TYR 0.018 0.001 TYR G 39 PHE 0.012 0.002 PHE H 62 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.17 (12951) covalent geometry : angle 0.56454 / 0.33 (18718) hydrogen bonds : bond 0.06764 / 4.56 ( 686) hydrogen bonds : angle 2.73525 / 1.94 ( 1746) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9179 (m-80) cc_final: 0.8954 (m-80) REVERT: C 74 LYS cc_start: 0.7430 (mtmp) cc_final: 0.7104 (mtmm) REVERT: E 134 ARG cc_start: 0.7608 (mtp85) cc_final: 0.7325 (mtp-110) REVERT: F 35 ARG cc_start: 0.7919 (mtt-85) cc_final: 0.7338 (mtm110) REVERT: H 81 ASN cc_start: 0.8317 (m-40) cc_final: 0.8062 (m-40) REVERT: H 89 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7731 (ptm-80) REVERT: H 96 ARG cc_start: 0.7725 (mtp180) cc_final: 0.7261 (mtm180) outliers start: 19 outliers final: 18 residues processed: 81 average time/residue: 0.1117 time to fit residues: 12.3074 Evaluate side-chains 84 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 97 optimal weight: 30.0000 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 101 optimal weight: 30.0000 chunk 35 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN G 38 ASN H 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.167760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.124791 restraints weight = 14782.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.123198 restraints weight = 26682.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.124177 restraints weight = 25012.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.124445 restraints weight = 19597.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.124521 restraints weight = 21228.833| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12951 Z= 0.127 Angle : 0.523 5.497 18718 Z= 0.318 Chirality : 0.038 0.308 2123 Planarity : 0.003 0.035 1365 Dihedral : 30.342 162.711 4077 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.16 % Allowed : 12.02 % Favored : 85.82 % 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: 2.41 (0.31), residues: 765 helix: 2.92 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.73 (0.34), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 20 TYR 0.011 0.001 TYR G 39 PHE 0.007 0.001 PHE H 62 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.13 (12951) covalent geometry : angle 0.52296 / 0.32 (18718) hydrogen bonds : bond 0.05863 / 3.96 ( 686) hydrogen bonds : angle 2.62891 / 1.87 ( 1746) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: C 74 LYS cc_start: 0.7458 (mtmp) cc_final: 0.6916 (mmmt) REVERT: E 134 ARG cc_start: 0.7625 (mtp85) cc_final: 0.7354 (mtp-110) REVERT: F 35 ARG cc_start: 0.7943 (mtt-85) cc_final: 0.7488 (mtm110) REVERT: H 81 ASN cc_start: 0.8210 (m-40) cc_final: 0.7938 (m-40) REVERT: H 89 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7746 (ptm-80) REVERT: H 96 ARG cc_start: 0.7725 (mtp180) cc_final: 0.7277 (mtm180) outliers start: 14 outliers final: 11 residues processed: 75 average time/residue: 0.1181 time to fit residues: 12.0527 Evaluate side-chains 75 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 89 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 0.0030 chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 30.0000 chunk 19 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.167901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.123603 restraints weight = 14851.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.122407 restraints weight = 24732.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.123348 restraints weight = 23306.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.123448 restraints weight = 19769.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.123730 restraints weight = 21236.655| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12951 Z= 0.122 Angle : 0.509 5.546 18718 Z= 0.311 Chirality : 0.038 0.305 2123 Planarity : 0.003 0.035 1365 Dihedral : 30.297 162.290 4077 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.31 % Allowed : 12.17 % Favored : 85.52 % 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: 2.57 (0.31), residues: 765 helix: 3.01 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.62 (0.35), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 35 TYR 0.012 0.001 TYR A 54 PHE 0.011 0.001 PHE F 100 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.12 (12951) covalent geometry : angle 0.50942 / 0.31 (18718) hydrogen bonds : bond 0.05432 / 3.68 ( 686) hydrogen bonds : angle 2.55812 / 1.82 ( 1746) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: E 134 ARG cc_start: 0.7674 (mtp85) cc_final: 0.7386 (mtp-110) REVERT: F 35 ARG cc_start: 0.7915 (mtt-85) cc_final: 0.7411 (mtm110) REVERT: H 81 ASN cc_start: 0.8084 (m-40) cc_final: 0.7794 (m-40) REVERT: H 89 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7676 (ptm-80) REVERT: H 96 ARG cc_start: 0.7676 (mtp180) cc_final: 0.7228 (mtm180) outliers start: 15 outliers final: 11 residues processed: 76 average time/residue: 0.1184 time to fit residues: 12.0453 Evaluate side-chains 75 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 89 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 80 optimal weight: 20.0000 chunk 86 optimal weight: 30.0000 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 98 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 chunk 30 optimal weight: 0.0570 chunk 5 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 chunk 94 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 overall best weight: 2.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.163323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.116186 restraints weight = 14695.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.115333 restraints weight = 30074.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.116446 restraints weight = 28972.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.116742 restraints weight = 22197.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.116936 restraints weight = 22916.490| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12951 Z= 0.200 Angle : 0.595 5.394 18718 Z= 0.347 Chirality : 0.042 0.312 2123 Planarity : 0.005 0.040 1365 Dihedral : 30.390 163.489 4077 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.16 % Allowed : 12.17 % Favored : 85.67 % 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: 2.05 (0.30), residues: 765 helix: 2.64 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.82 (0.34), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 35 TYR 0.020 0.002 TYR A 54 PHE 0.015 0.002 PHE H 62 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (12951) covalent geometry : angle 0.59451 / 0.35 (18718) hydrogen bonds : bond 0.07186 / 4.84 ( 686) hydrogen bonds : angle 2.78578 / 1.99 ( 1746) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1401.85 seconds wall clock time: 24 minutes 49.64 seconds (1489.64 seconds total)