Starting phenix.real_space_refine on Fri Sep 11 21:01:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v90_31806/09_2026/7v90_31806.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v90_31806/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7v90_31806/09_2026/7v90_31806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v90_31806/09_2026/7v90_31806.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v90_31806/09_2026/7v90_31806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v90_31806/09_2026/7v90_31806.map" } 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-2.2.1-6174/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: 3.04, per 1000 atoms: 0.25 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: 1.09 Conformation dependent library (CDL) restraints added in 425.9 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: 2.00 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: 2.06 Time building geometry restraints manager: 1.52 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=" O3' DG I 12 " pdb=" P DG I 13 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.20e-02 6.94e+03 1.79e+01 bond pdb=" O3' DG I -66 " pdb=" P DG I -65 " ideal model delta sigma weight residual 1.607 1.654 -0.047 1.20e-02 6.94e+03 1.56e+01 bond pdb=" O3' DG I 32 " pdb=" P DT I 33 " ideal model delta sigma weight residual 1.607 1.650 -0.043 1.20e-02 6.94e+03 1.28e+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 ... (remaining 12946 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 17946 2.16 - 4.33: 731 4.33 - 6.49: 34 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.390 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.710 ------------------------------------------------------------------------------- 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= 0.562 Angle : 0.844 10.814 18718 Z= 0.722 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 0.84376 / 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 : 0.311 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8084 (mtpp) cc_final: 0.7695 (mttp) REVERT: C 15 LYS cc_start: 0.7457 (mtpp) cc_final: 0.7039 (tttp) REVERT: D 30 ARG cc_start: 0.5004 (ptm-80) cc_final: 0.4201 (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: 0.7559 (tttt) REVERT: H 25 LYS cc_start: 0.3299 (OUTLIER) cc_final: 0.2129 (ptmt) outliers start: 26 outliers final: 4 residues processed: 141 average time/residue: 0.1998 time to fit residues: 34.9930 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 : 0.320 ------------------------------------------------------------------------------- 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: 10.0000 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 = 0.4006 r_free = 0.4006 target = 0.182277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.139394 restraints weight = 15348.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.138616 restraints weight = 26829.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.139174 restraints weight = 25128.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.139286 restraints weight = 20449.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.139530 restraints weight = 18459.263| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12951 Z= 0.146 Angle : 0.572 6.226 18718 Z= 0.356 Chirality : 0.040 0.308 2123 Planarity : 0.004 0.036 1365 Dihedral : 29.713 155.146 4091 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.40 % Favored : 96.34 % Rotamer: Outliers : 2.00 % Allowed : 8.47 % Favored : 89.52 % 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: 1.08 (0.29), residues: 765 helix: 1.84 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -2.14 (0.32), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 77 TYR 0.021 0.001 TYR D 34 PHE 0.006 0.001 PHE F 61 HIS 0.004 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.15 (12951) covalent geometry : angle 0.57222 / 0.36 (18718) hydrogen bonds : bond 0.05671 / 4.00 ( 686) hydrogen bonds : angle 2.57500 / 1.88 ( 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 86 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: D 28 ARG cc_start: 0.4712 (OUTLIER) cc_final: 0.4469 (ptp-170) REVERT: D 30 ARG cc_start: 0.6089 (ptm-80) cc_final: 0.5230 (mtp180) REVERT: F 35 ARG cc_start: 0.7871 (mtt-85) cc_final: 0.7609 (mtm110) REVERT: G 15 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7908 (tttt) REVERT: H 98 LEU cc_start: 0.8786 (mm) cc_final: 0.8569 (mm) outliers start: 13 outliers final: 6 residues processed: 83 average time/residue: 0.1572 time to fit residues: 17.3280 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 : 0.302 ------------------------------------------------------------------------------- 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: 7.9990 chunk 44 optimal weight: 0.0970 chunk 35 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 81 optimal weight: 30.0000 chunk 34 optimal weight: 3.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.173046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.129491 restraints weight = 15061.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.127631 restraints weight = 26605.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.128587 restraints weight = 25294.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.128832 restraints weight = 19642.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.128919 restraints weight = 21235.407| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12951 Z= 0.154 Angle : 0.581 6.939 18718 Z= 0.346 Chirality : 0.040 0.331 2123 Planarity : 0.004 0.047 1365 Dihedral : 30.280 157.671 4077 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.53 % Favored : 96.21 % Rotamer: Outliers : 1.69 % Allowed : 8.78 % Favored : 89.52 % 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: 1.87 (0.30), residues: 765 helix: 2.41 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.73 (0.34), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG C 20 TYR 0.013 0.002 TYR A 54 PHE 0.013 0.002 PHE H 62 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 (12951) covalent geometry : angle 0.58073 / 0.35 (18718) hydrogen bonds : bond 0.06373 / 4.32 ( 686) hydrogen bonds : angle 2.58339 / 1.85 ( 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 85 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: D 30 ARG cc_start: 0.5918 (ptm-80) cc_final: 0.5094 (mtt180) REVERT: F 35 ARG cc_start: 0.7886 (mtt-85) cc_final: 0.7529 (mtm110) REVERT: H 96 ARG cc_start: 0.7807 (mtp180) cc_final: 0.7502 (mtm180) outliers start: 11 outliers final: 8 residues processed: 81 average time/residue: 0.1519 time to fit residues: 16.4215 Evaluate side-chains 78 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR 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 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: 1.9990 chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 73 ASN D 46 HIS F 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.164415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.120958 restraints weight = 14867.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.118935 restraints weight = 25767.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.119979 restraints weight = 23979.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.120476 restraints weight = 17996.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.120776 restraints weight = 17603.243| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12951 Z= 0.197 Angle : 0.656 6.381 18718 Z= 0.376 Chirality : 0.045 0.354 2123 Planarity : 0.005 0.041 1365 Dihedral : 30.438 161.278 4077 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.79 % Favored : 95.95 % Rotamer: Outliers : 2.31 % Allowed : 9.71 % 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: 1.53 (0.30), residues: 765 helix: 2.22 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -2.00 (0.34), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 20 TYR 0.020 0.002 TYR D 34 PHE 0.018 0.002 PHE H 62 HIS 0.007 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (12951) covalent geometry : angle 0.65565 / 0.38 (18718) hydrogen bonds : bond 0.08142 / 5.51 ( 686) hydrogen bonds : angle 2.92408 / 2.10 ( 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 90 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9227 (m-80) cc_final: 0.8896 (m-80) REVERT: A 109 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8163 (mp) REVERT: C 74 LYS cc_start: 0.7285 (mtmp) cc_final: 0.7043 (mtmm) REVERT: D 30 ARG cc_start: 0.5939 (ptm-80) cc_final: 0.5050 (mtp180) REVERT: F 35 ARG cc_start: 0.7960 (mtt-85) cc_final: 0.7425 (mtm110) REVERT: H 96 ARG cc_start: 0.7801 (mtp180) cc_final: 0.7427 (mtm180) outliers start: 15 outliers final: 12 residues processed: 86 average time/residue: 0.1374 time to fit residues: 15.8286 Evaluate side-chains 80 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 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 E residue 118 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 H residue 36 VAL 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: 0.7980 chunk 17 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 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: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.167031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.122656 restraints weight = 14911.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.121169 restraints weight = 25601.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.122073 restraints weight = 22358.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.122156 restraints weight = 18334.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.122465 restraints weight = 19202.414| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3314 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= 0.135 Angle : 0.550 5.762 18718 Z= 0.330 Chirality : 0.039 0.341 2123 Planarity : 0.004 0.035 1365 Dihedral : 30.307 161.071 4077 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.01 % Favored : 96.86 % Rotamer: Outliers : 2.00 % Allowed : 10.32 % Favored : 87.67 % 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: 2.10 (0.31), residues: 765 helix: 2.66 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.82 (0.34), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 40 TYR 0.011 0.001 TYR D 34 PHE 0.009 0.001 PHE F 100 HIS 0.014 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.14 (12951) covalent geometry : angle 0.55038 / 0.33 (18718) hydrogen bonds : bond 0.06404 / 4.32 ( 686) hydrogen bonds : angle 2.69199 / 1.92 ( 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 82 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9167 (m-80) cc_final: 0.8947 (m-80) REVERT: B 92 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7761 (ttp80) REVERT: C 38 ASN cc_start: 0.8260 (t0) cc_final: 0.8049 (m-40) REVERT: C 74 LYS cc_start: 0.7416 (mtmp) cc_final: 0.7122 (mtmm) REVERT: D 30 ARG cc_start: 0.5893 (ptm-80) cc_final: 0.5113 (mtp180) REVERT: F 35 ARG cc_start: 0.7918 (mtt-85) cc_final: 0.7447 (mtm110) REVERT: H 81 ASN cc_start: 0.8443 (m-40) cc_final: 0.8158 (m-40) REVERT: H 96 ARG cc_start: 0.7736 (mtp180) cc_final: 0.7328 (mtm180) outliers start: 13 outliers final: 11 residues processed: 79 average time/residue: 0.1517 time to fit residues: 16.0425 Evaluate side-chains 78 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR 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 35 ARG Chi-restraints excluded: chain G residue 101 THR 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: 10.0000 chunk 4 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 72 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN 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 = 0.167318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.123039 restraints weight = 14895.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.121615 restraints weight = 25266.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.122549 restraints weight = 22664.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.122676 restraints weight = 18355.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.123062 restraints weight = 18874.236| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3407 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= 0.137 Angle : 0.540 5.678 18718 Z= 0.322 Chirality : 0.039 0.338 2123 Planarity : 0.004 0.036 1365 Dihedral : 30.300 161.251 4077 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.27 % Favored : 96.60 % Rotamer: Outliers : 2.47 % Allowed : 10.79 % Favored : 86.75 % 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: 2.30 (0.31), residues: 765 helix: 2.79 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.70 (0.35), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 20 TYR 0.010 0.001 TYR F 51 PHE 0.011 0.001 PHE F 100 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (12951) covalent geometry : angle 0.54034 / 0.32 (18718) hydrogen bonds : bond 0.06009 / 4.07 ( 686) hydrogen bonds : angle 2.60157 / 1.85 ( 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 84 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9171 (m-80) cc_final: 0.8966 (m-80) REVERT: C 38 ASN cc_start: 0.8252 (t0) cc_final: 0.8031 (m-40) REVERT: D 30 ARG cc_start: 0.5855 (ptm-80) cc_final: 0.5001 (mtp180) REVERT: F 35 ARG cc_start: 0.7944 (mtt-85) cc_final: 0.7456 (mtm110) REVERT: H 81 ASN cc_start: 0.8324 (m-40) cc_final: 0.7987 (m-40) REVERT: H 96 ARG cc_start: 0.7702 (mtp180) cc_final: 0.7272 (mtm180) outliers start: 16 outliers final: 14 residues processed: 80 average time/residue: 0.1371 time to fit residues: 14.8981 Evaluate side-chains 79 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR 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 119 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG 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 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 5 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 93 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN H 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.167561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.123123 restraints weight = 14855.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.121645 restraints weight = 25131.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.122545 restraints weight = 24161.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.122773 restraints weight = 18963.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.122903 restraints weight = 20404.462| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12951 Z= 0.133 Angle : 0.534 6.482 18718 Z= 0.320 Chirality : 0.039 0.337 2123 Planarity : 0.004 0.034 1365 Dihedral : 30.272 161.242 4077 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.62 % Allowed : 10.79 % Favored : 86.59 % 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: 2.44 (0.31), residues: 765 helix: 2.89 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.58 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 20 TYR 0.012 0.001 TYR E 41 PHE 0.009 0.001 PHE H 62 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 (12951) covalent geometry : angle 0.53429 / 0.32 (18718) hydrogen bonds : bond 0.05850 / 3.96 ( 686) hydrogen bonds : angle 2.58226 / 1.84 ( 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 82 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9169 (m-80) cc_final: 0.8947 (m-80) REVERT: F 35 ARG cc_start: 0.7897 (mtt-85) cc_final: 0.7407 (mtm110) REVERT: H 73 GLU cc_start: 0.8607 (tp30) cc_final: 0.8304 (tp30) REVERT: H 81 ASN cc_start: 0.8247 (m-40) cc_final: 0.7916 (m-40) REVERT: H 89 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7759 (ptm-80) REVERT: H 96 ARG cc_start: 0.7709 (mtp180) cc_final: 0.7271 (mtm180) outliers start: 17 outliers final: 13 residues processed: 78 average time/residue: 0.1442 time to fit residues: 15.3435 Evaluate side-chains 79 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 16 THR 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 35 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 99 optimal weight: 30.0000 chunk 73 optimal weight: 5.9990 chunk 84 optimal weight: 30.0000 chunk 36 optimal weight: 2.9990 chunk 94 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.161037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.117514 restraints weight = 14815.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.115924 restraints weight = 24832.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.116923 restraints weight = 20765.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.117288 restraints weight = 16922.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.117766 restraints weight = 16934.034| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12951 Z= 0.237 Angle : 0.680 6.026 18718 Z= 0.383 Chirality : 0.047 0.359 2123 Planarity : 0.006 0.048 1365 Dihedral : 30.449 163.605 4077 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.62 % Allowed : 10.94 % Favored : 86.44 % 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: 1.58 (0.30), residues: 765 helix: 2.29 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.99 (0.33), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 131 TYR 0.016 0.002 TYR D 34 PHE 0.019 0.002 PHE H 62 HIS 0.006 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.24 (12951) covalent geometry : angle 0.67973 / 0.38 (18718) hydrogen bonds : bond 0.08594 / 5.77 ( 686) hydrogen bonds : angle 2.99905 / 2.14 ( 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: 17 poor density : 68 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9222 (m-80) cc_final: 0.8975 (m-80) REVERT: C 38 ASN cc_start: 0.8402 (t0) cc_final: 0.8163 (m-40) REVERT: C 74 LYS cc_start: 0.7510 (mtmp) cc_final: 0.7180 (mtmm) REVERT: E 134 ARG cc_start: 0.7402 (ttm-80) cc_final: 0.7098 (ttp80) REVERT: F 35 ARG cc_start: 0.7881 (mtt-85) cc_final: 0.7265 (mtm-85) REVERT: H 73 GLU cc_start: 0.8614 (tp30) cc_final: 0.8364 (tp30) REVERT: H 81 ASN cc_start: 0.8649 (m-40) cc_final: 0.8410 (m-40) REVERT: H 89 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7657 (ptm-80) REVERT: H 96 ARG cc_start: 0.7734 (mtp180) cc_final: 0.7283 (mtm180) REVERT: H 109 SER cc_start: 0.8405 (t) cc_final: 0.8186 (m) outliers start: 17 outliers final: 15 residues processed: 83 average time/residue: 0.1489 time to fit residues: 16.7009 Evaluate side-chains 79 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 F residue 95 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 97 optimal weight: 30.0000 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 101 optimal weight: 40.0000 chunk 35 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.164763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.120058 restraints weight = 14732.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.118694 restraints weight = 25042.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.119559 restraints weight = 23282.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.119675 restraints weight = 19763.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.119998 restraints weight = 21012.469| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12951 Z= 0.135 Angle : 0.563 5.857 18718 Z= 0.334 Chirality : 0.041 0.353 2123 Planarity : 0.004 0.035 1365 Dihedral : 30.294 162.776 4077 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.39 % Allowed : 11.86 % Favored : 86.75 % 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: 2.18 (0.31), residues: 765 helix: 2.75 (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 0.012 0.001 TYR D 34 PHE 0.008 0.001 PHE F 100 HIS 0.002 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.13 (12951) covalent geometry : angle 0.56254 / 0.33 (18718) hydrogen bonds : bond 0.06540 / 4.39 ( 686) hydrogen bonds : angle 2.73869 / 1.95 ( 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 75 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9153 (m-80) cc_final: 0.8946 (m-80) REVERT: C 38 ASN cc_start: 0.8324 (t0) cc_final: 0.8093 (m-40) REVERT: C 74 LYS cc_start: 0.7521 (mtmp) cc_final: 0.7200 (mtmm) REVERT: F 35 ARG cc_start: 0.7889 (mtt-85) cc_final: 0.7329 (mtm110) REVERT: H 81 ASN cc_start: 0.8457 (m-40) cc_final: 0.8196 (m-40) REVERT: H 89 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7694 (ptm-80) REVERT: H 96 ARG cc_start: 0.7698 (mtp180) cc_final: 0.7239 (mtm180) outliers start: 9 outliers final: 8 residues processed: 72 average time/residue: 0.1580 time to fit residues: 15.2903 Evaluate side-chains 75 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 56 MET 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 62 ILE Chi-restraints excluded: chain H residue 56 MET 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: 0.0870 chunk 55 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 92 optimal weight: 30.0000 chunk 19 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.167181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.120580 restraints weight = 14878.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.120062 restraints weight = 28631.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.121085 restraints weight = 30650.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.121119 restraints weight = 24464.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.121313 restraints weight = 26498.907| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3872 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= 0.124 Angle : 0.523 5.771 18718 Z= 0.315 Chirality : 0.039 0.336 2123 Planarity : 0.004 0.035 1365 Dihedral : 30.239 162.125 4077 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.92 % Allowed : 12.17 % 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: 2.54 (0.31), residues: 765 helix: 3.01 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.65 (0.35), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 20 TYR 0.010 0.001 TYR F 51 PHE 0.008 0.001 PHE F 100 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.12 (12951) covalent geometry : angle 0.52286 / 0.32 (18718) hydrogen bonds : bond 0.05464 / 3.69 ( 686) hydrogen bonds : angle 2.55928 / 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 71 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9131 (m-80) cc_final: 0.8928 (m-80) REVERT: F 35 ARG cc_start: 0.7893 (mtt-85) cc_final: 0.7437 (mtm110) REVERT: G 104 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8130 (mm-40) REVERT: H 81 ASN cc_start: 0.8187 (m-40) cc_final: 0.7877 (m-40) REVERT: H 89 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7792 (ptm-80) REVERT: H 96 ARG cc_start: 0.7669 (mtp180) cc_final: 0.7206 (mtm180) outliers start: 6 outliers final: 5 residues processed: 70 average time/residue: 0.1716 time to fit residues: 15.8819 Evaluate side-chains 70 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 95 ARG 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: 2.9990 chunk 64 optimal weight: 0.0050 chunk 98 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 55 optimal weight: 0.0470 chunk 94 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 overall best weight: 2.2098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.163751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.119175 restraints weight = 14762.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.117720 restraints weight = 24906.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.118583 restraints weight = 22352.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.118767 restraints weight = 18513.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.119195 restraints weight = 18802.435| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4058 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= 0.165 Angle : 0.581 5.604 18718 Z= 0.338 Chirality : 0.041 0.339 2123 Planarity : 0.004 0.040 1365 Dihedral : 30.309 162.454 4077 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.39 % Allowed : 11.86 % Favored : 86.75 % 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: 2.16 (0.30), residues: 765 helix: 2.71 (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 0.007 0.001 ARG C 20 TYR 0.013 0.001 TYR F 51 PHE 0.014 0.002 PHE H 62 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (12951) covalent geometry : angle 0.58087 / 0.34 (18718) hydrogen bonds : bond 0.06806 / 4.58 ( 686) hydrogen bonds : angle 2.74701 / 1.96 ( 1746) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1676.80 seconds wall clock time: 29 minutes 38.09 seconds (1778.09 seconds total)